diff --git a/assets/img/faq/how_are_the_lpa_and_rpa_points_defined/ear_molds_1.jpg b/assets/img/faq/anat_dicom2ctf/ear_molds_1.jpg similarity index 100% rename from assets/img/faq/how_are_the_lpa_and_rpa_points_defined/ear_molds_1.jpg rename to assets/img/faq/anat_dicom2ctf/ear_molds_1.jpg diff --git a/assets/img/faq/how_are_the_lpa_and_rpa_points_defined/ear_molds_2.jpg b/assets/img/faq/anat_dicom2ctf/ear_molds_2.jpg similarity index 100% rename from assets/img/faq/how_are_the_lpa_and_rpa_points_defined/ear_molds_2.jpg rename to assets/img/faq/anat_dicom2ctf/ear_molds_2.jpg diff --git a/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/fiducials1.png b/assets/img/faq/anat_dicom2ctf/fiducials1.png similarity index 100% rename from assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/fiducials1.png rename to assets/img/faq/anat_dicom2ctf/fiducials1.png diff --git a/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/fiducials2.png b/assets/img/faq/anat_dicom2ctf/fiducials2.png similarity index 100% rename from assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/fiducials2.png rename to assets/img/faq/anat_dicom2ctf/fiducials2.png diff --git a/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/fiducials3.png b/assets/img/faq/anat_dicom2ctf/fiducials3.png similarity index 100% rename from assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/fiducials3.png rename to assets/img/faq/anat_dicom2ctf/fiducials3.png diff --git a/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/vitamine_marker1.png b/assets/img/faq/anat_dicom2ctf/vitamine_marker1.png similarity index 100% rename from assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/vitamine_marker1.png rename to assets/img/faq/anat_dicom2ctf/vitamine_marker1.png diff --git a/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/vitamine_marker2.png b/assets/img/faq/anat_dicom2ctf/vitamine_marker2.png similarity index 100% rename from assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/vitamine_marker2.png rename to assets/img/faq/anat_dicom2ctf/vitamine_marker2.png diff --git a/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/vitamine_marker3.png b/assets/img/faq/anat_dicom2ctf/vitamine_marker3.png similarity index 100% rename from assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/vitamine_marker3.png rename to assets/img/faq/anat_dicom2ctf/vitamine_marker3.png diff --git a/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/ear_molds_1.jpg b/assets/img/faq/anat_landmarks/ear_molds_1.jpg similarity index 100% rename from assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/ear_molds_1.jpg rename to assets/img/faq/anat_landmarks/ear_molds_1.jpg diff --git a/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/ear_molds_2.jpg b/assets/img/faq/anat_landmarks/ear_molds_2.jpg similarity index 100% rename from assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/ear_molds_2.jpg rename to assets/img/faq/anat_landmarks/ear_molds_2.jpg diff --git a/assets/img/faq/how_are_the_lpa_and_rpa_points_defined/tragus.png b/assets/img/faq/anat_landmarks/tragus.png similarity index 100% rename from assets/img/faq/how_are_the_lpa_and_rpa_points_defined/tragus.png rename to assets/img/faq/anat_landmarks/tragus.png diff --git a/assets/img/faq/how_are_the_lpa_and_rpa_points_defined/zygomatic_arch.png b/assets/img/faq/anat_landmarks/zygomatic_arch.png similarity index 100% rename from assets/img/faq/how_are_the_lpa_and_rpa_points_defined/zygomatic_arch.png rename to assets/img/faq/anat_landmarks/zygomatic_arch.png diff --git a/assets/img/faq/how_change_mri_orientation_size_fov/mri.png b/assets/img/faq/anat_reslice/mri.png similarity index 100% rename from assets/img/faq/how_change_mri_orientation_size_fov/mri.png rename to assets/img/faq/anat_reslice/mri.png diff --git a/assets/img/faq/how_change_mri_orientation_size_fov/mrirs.png b/assets/img/faq/anat_reslice/mrirs.png similarity index 100% rename from assets/img/faq/how_change_mri_orientation_size_fov/mrirs.png rename to assets/img/faq/anat_reslice/mrirs.png diff --git a/assets/img/faq/how_change_mri_orientation_size_fov/reslice2.jpg b/assets/img/faq/anat_reslice/reslice2.jpg similarity index 100% rename from assets/img/faq/how_change_mri_orientation_size_fov/reslice2.jpg rename to assets/img/faq/anat_reslice/reslice2.jpg diff --git a/assets/img/faq/my_mri_is_upside_down_is_this_a_problem/potatomen.png b/assets/img/faq/anat_upsidedown/potatomen.png similarity index 100% rename from assets/img/faq/my_mri_is_upside_down_is_this_a_problem/potatomen.png rename to assets/img/faq/anat_upsidedown/potatomen.png diff --git a/assets/img/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot/correct_sourceplot.png b/assets/img/faq/anat_upsidedownplotting/correct_sourceplot.png similarity index 100% rename from assets/img/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot/correct_sourceplot.png rename to assets/img/faq/anat_upsidedownplotting/correct_sourceplot.png diff --git a/assets/img/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot/upside_down_sourceplot.png b/assets/img/faq/anat_upsidedownplotting/upside_down_sourceplot.png similarity index 100% rename from assets/img/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot/upside_down_sourceplot.png rename to assets/img/faq/anat_upsidedownplotting/upside_down_sourceplot.png diff --git a/assets/img/faq/how_can_i_anonymize_an_anatomical_mri/defacevolume1.png b/assets/img/faq/anonymization_anatomical/defacevolume1.png similarity index 100% rename from assets/img/faq/how_can_i_anonymize_an_anatomical_mri/defacevolume1.png rename to assets/img/faq/anonymization_anatomical/defacevolume1.png diff --git a/assets/img/faq/how_can_i_anonymize_an_anatomical_mri/defacevolume2.png b/assets/img/faq/anonymization_anatomical/defacevolume2.png similarity index 100% rename from assets/img/faq/how_can_i_anonymize_an_anatomical_mri/defacevolume2.png rename to assets/img/faq/anonymization_anatomical/defacevolume2.png diff --git a/assets/img/faq/how_can_i_anonymize_an_anatomical_mri/defacevolume3.png b/assets/img/faq/anonymization_anatomical/defacevolume3.png similarity index 100% rename from assets/img/faq/how_can_i_anonymize_an_anatomical_mri/defacevolume3.png rename to assets/img/faq/anonymization_anatomical/defacevolume3.png diff --git a/assets/img/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts/padding_fig1.png b/assets/img/faq/artifact_padding/padding_fig1.png similarity index 100% rename from assets/img/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts/padding_fig1.png rename to assets/img/faq/artifact_padding/padding_fig1.png diff --git a/assets/img/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts/padding_fig2.png b/assets/img/faq/artifact_padding/padding_fig2.png similarity index 100% rename from assets/img/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts/padding_fig2.png rename to assets/img/faq/artifact_padding/padding_fig2.png diff --git a/assets/img/faq/how_can_i_fine-tune_my_bem_volume_conduction_model/wiki12.png b/assets/img/faq/bem_finetune/wiki12.png similarity index 100% rename from assets/img/faq/how_can_i_fine-tune_my_bem_volume_conduction_model/wiki12.png rename to assets/img/faq/bem_finetune/wiki12.png diff --git a/assets/img/faq/how_can_i_fine-tune_my_bem_volume_conduction_model/wiki34.png b/assets/img/faq/bem_finetune/wiki34.png similarity index 100% rename from assets/img/faq/how_can_i_fine-tune_my_bem_volume_conduction_model/wiki34.png rename to assets/img/faq/bem_finetune/wiki34.png diff --git a/assets/img/faq/how_does_the_ctf_higher-order_gradiometer_work/g1brv.png b/assets/img/faq/ctf_syntheticgradient/g1brv.png similarity index 100% rename from assets/img/faq/how_does_the_ctf_higher-order_gradiometer_work/g1brv.png rename to assets/img/faq/ctf_syntheticgradient/g1brv.png diff --git a/assets/img/faq/how_does_the_ctf_higher-order_gradiometer_work/g2brv.png b/assets/img/faq/ctf_syntheticgradient/g2brv.png similarity index 100% rename from assets/img/faq/how_does_the_ctf_higher-order_gradiometer_work/g2brv.png rename to assets/img/faq/ctf_syntheticgradient/g2brv.png diff --git a/assets/img/faq/how_does_the_ctf_higher-order_gradiometer_work/g3brv.png b/assets/img/faq/ctf_syntheticgradient/g3brv.png similarity index 100% rename from assets/img/faq/how_does_the_ctf_higher-order_gradiometer_work/g3brv.png rename to assets/img/faq/ctf_syntheticgradient/g3brv.png diff --git a/assets/img/faq/how_is_the_segmentation_defined/afni_atlas.png b/assets/img/faq/datatype_segmentation/afni_atlas.png similarity index 100% rename from assets/img/faq/how_is_the_segmentation_defined/afni_atlas.png rename to assets/img/faq/datatype_segmentation/afni_atlas.png diff --git a/assets/img/faq/how_is_the_segmentation_defined/brain.png b/assets/img/faq/datatype_segmentation/brain.png similarity index 100% rename from assets/img/faq/how_is_the_segmentation_defined/brain.png rename to assets/img/faq/datatype_segmentation/brain.png diff --git a/assets/img/faq/how_is_the_segmentation_defined/csf.png b/assets/img/faq/datatype_segmentation/csf.png similarity index 100% rename from assets/img/faq/how_is_the_segmentation_defined/csf.png rename to assets/img/faq/datatype_segmentation/csf.png diff --git a/assets/img/faq/how_is_the_segmentation_defined/gray.png b/assets/img/faq/datatype_segmentation/gray.png similarity index 100% rename from assets/img/faq/how_is_the_segmentation_defined/gray.png rename to assets/img/faq/datatype_segmentation/gray.png diff --git a/assets/img/faq/how_is_the_segmentation_defined/scalp.png b/assets/img/faq/datatype_segmentation/scalp.png similarity index 100% rename from assets/img/faq/how_is_the_segmentation_defined/scalp.png rename to assets/img/faq/datatype_segmentation/scalp.png diff --git a/assets/img/faq/how_is_the_segmentation_defined/scalponly.png b/assets/img/faq/datatype_segmentation/scalponly.png similarity index 100% rename from assets/img/faq/how_is_the_segmentation_defined/scalponly.png rename to assets/img/faq/datatype_segmentation/scalponly.png diff --git a/assets/img/faq/how_is_the_segmentation_defined/seg_indexed.png b/assets/img/faq/datatype_segmentation/seg_indexed.png similarity index 100% rename from assets/img/faq/how_is_the_segmentation_defined/seg_indexed.png rename to assets/img/faq/datatype_segmentation/seg_indexed.png diff --git a/assets/img/faq/how_is_the_segmentation_defined/skull.png b/assets/img/faq/datatype_segmentation/skull.png similarity index 100% rename from assets/img/faq/how_is_the_segmentation_defined/skull.png rename to assets/img/faq/datatype_segmentation/skull.png diff --git a/assets/img/faq/how_is_the_segmentation_defined/tissue_representation.png b/assets/img/faq/datatype_segmentation/tissue_representation.png similarity index 100% rename from assets/img/faq/how_is_the_segmentation_defined/tissue_representation.png rename to assets/img/faq/datatype_segmentation/tissue_representation.png diff --git a/assets/img/faq/how_is_the_segmentation_defined/white.png b/assets/img/faq/datatype_segmentation/white.png similarity index 100% rename from assets/img/faq/how_is_the_segmentation_defined/white.png rename to assets/img/faq/datatype_segmentation/white.png diff --git a/assets/img/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter/dftfilter1.png b/assets/img/faq/dftfilter_residual/dftfilter1.png similarity index 100% rename from assets/img/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter/dftfilter1.png rename to assets/img/faq/dftfilter_residual/dftfilter1.png diff --git a/assets/img/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter/dftfilter2.png b/assets/img/faq/dftfilter_residual/dftfilter2.png similarity index 100% rename from assets/img/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter/dftfilter2.png rename to assets/img/faq/dftfilter_residual/dftfilter2.png diff --git a/assets/img/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter/linenoise.png b/assets/img/faq/dftfilter_residual/linenoise.png similarity index 100% rename from assets/img/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter/linenoise.png rename to assets/img/faq/dftfilter_residual/linenoise.png diff --git a/assets/img/faq/how_to_ask_good_questions_to_the_community/peanutsediting.jpg b/assets/img/faq/emaillist_howtoask/peanutsediting.jpg similarity index 100% rename from assets/img/faq/how_to_ask_good_questions_to_the_community/peanutsediting.jpg rename to assets/img/faq/emaillist_howtoask/peanutsediting.jpg diff --git a/assets/img/faq/what_is_the_relation_between_events_such_as_triggers_and_trials/offset.png b/assets/img/faq/eventsversustrials/offset.png similarity index 100% rename from assets/img/faq/what_is_the_relation_between_events_such_as_triggers_and_trials/offset.png rename to assets/img/faq/eventsversustrials/offset.png diff --git a/assets/img/faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head/fiducial_points.png b/assets/img/faq/fiducials_definition/fiducial_points.png similarity index 100% rename from assets/img/faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head/fiducial_points.png rename to assets/img/faq/fiducials_definition/fiducial_points.png diff --git a/assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/bufferviewer.png b/assets/img/faq/fieldtripbuffer_gettingstarted/bufferviewer.png similarity index 100% rename from assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/bufferviewer.png rename to assets/img/faq/fieldtripbuffer_gettingstarted/bufferviewer.png diff --git a/assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/bufferviewer_running.png b/assets/img/faq/fieldtripbuffer_gettingstarted/bufferviewer_running.png similarity index 100% rename from assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/bufferviewer_running.png rename to assets/img/faq/fieldtripbuffer_gettingstarted/bufferviewer_running.png diff --git a/assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/screen_shot_2013-11-12_at_17.05.01.png b/assets/img/faq/fieldtripbuffer_gettingstarted/screen_shot_2013-11-12_at_17.05.01.png similarity index 100% rename from assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/screen_shot_2013-11-12_at_17.05.01.png rename to assets/img/faq/fieldtripbuffer_gettingstarted/screen_shot_2013-11-12_at_17.05.01.png diff --git a/assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/sine2ft.png b/assets/img/faq/fieldtripbuffer_gettingstarted/sine2ft.png similarity index 100% rename from assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/sine2ft.png rename to assets/img/faq/fieldtripbuffer_gettingstarted/sine2ft.png diff --git a/assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/sine2ft_running.png b/assets/img/faq/fieldtripbuffer_gettingstarted/sine2ft_running.png similarity index 100% rename from assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/sine2ft_running.png rename to assets/img/faq/fieldtripbuffer_gettingstarted/sine2ft_running.png diff --git a/assets/img/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming/benchmark_r.png b/assets/img/faq/fieldtripbuffer_speed/benchmark_r.png similarity index 100% rename from assets/img/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming/benchmark_r.png rename to assets/img/faq/fieldtripbuffer_speed/benchmark_r.png diff --git a/assets/img/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming/benchmark_w.png b/assets/img/faq/fieldtripbuffer_speed/benchmark_w.png similarity index 100% rename from assets/img/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming/benchmark_w.png rename to assets/img/faq/fieldtripbuffer_speed/benchmark_w.png diff --git a/assets/img/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming/mentat201_tcp_vs_unix.png b/assets/img/faq/fieldtripbuffer_speed/mentat201_tcp_vs_unix.png similarity index 100% rename from assets/img/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming/mentat201_tcp_vs_unix.png rename to assets/img/faq/fieldtripbuffer_speed/mentat201_tcp_vs_unix.png diff --git a/assets/img/faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session/anims1.gif b/assets/img/faq/headlocalizer/anims1.gif similarity index 100% rename from assets/img/faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session/anims1.gif rename to assets/img/faq/headlocalizer/anims1.gif diff --git a/assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd0.png b/assets/img/faq/headmodel_meshingproblem/bnd0.png similarity index 100% rename from assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd0.png rename to assets/img/faq/headmodel_meshingproblem/bnd0.png diff --git a/assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd1.png b/assets/img/faq/headmodel_meshingproblem/bnd1.png similarity index 100% rename from assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd1.png rename to assets/img/faq/headmodel_meshingproblem/bnd1.png diff --git a/assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd2.png b/assets/img/faq/headmodel_meshingproblem/bnd2.png similarity index 100% rename from assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd2.png rename to assets/img/faq/headmodel_meshingproblem/bnd2.png diff --git a/assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd3.png b/assets/img/faq/headmodel_meshingproblem/bnd3.png similarity index 100% rename from assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd3.png rename to assets/img/faq/headmodel_meshingproblem/bnd3.png diff --git a/assets/img/faq/why_does_my_eegheadmodel_look_funny/inhomogeneity.png b/assets/img/faq/headmodel_meshingproblem/inhomogeneity.png similarity index 100% rename from assets/img/faq/why_does_my_eegheadmodel_look_funny/inhomogeneity.png rename to assets/img/faq/headmodel_meshingproblem/inhomogeneity.png diff --git a/assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/correlation.png b/assets/img/faq/ica_rereference/correlation.png similarity index 100% rename from assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/correlation.png rename to assets/img/faq/ica_rereference/correlation.png diff --git a/assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/correlation_sorted.png b/assets/img/faq/ica_rereference/correlation_sorted.png similarity index 100% rename from assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/correlation_sorted.png rename to assets/img/faq/ica_rereference/correlation_sorted.png diff --git a/assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/multiplot.png b/assets/img/faq/ica_rereference/multiplot.png similarity index 100% rename from assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/multiplot.png rename to assets/img/faq/ica_rereference/multiplot.png diff --git a/assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/singleplot_FC1.png b/assets/img/faq/ica_rereference/singleplot_FC1.png similarity index 100% rename from assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/singleplot_FC1.png rename to assets/img/faq/ica_rereference/singleplot_FC1.png diff --git a/assets/img/faq/how_can_i_inspect_the_electrode_impedances_of_my_data/impedance.png b/assets/img/faq/impedancecheck/impedance.png similarity index 100% rename from assets/img/faq/how_can_i_inspect_the_electrode_impedances_of_my_data/impedance.png rename to assets/img/faq/impedancecheck/impedance.png diff --git a/assets/img/faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified/screenshot.png b/assets/img/faq/mex_osx/screenshot.png similarity index 100% rename from assets/img/faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified/screenshot.png rename to assets/img/faq/mex_osx/screenshot.png diff --git a/assets/img/faq/how_can_i_visualize_the_neuromag_head_position_indicator_coils/neuromag_wikiexample.png b/assets/img/faq/neuromag_hpi/neuromag_wikiexample.png similarity index 100% rename from assets/img/faq/how_can_i_visualize_the_neuromag_head_position_indicator_coils/neuromag_wikiexample.png rename to assets/img/faq/neuromag_hpi/neuromag_wikiexample.png diff --git a/assets/img/faq/how_can_i_test_the_serial_port_connection_between_two_computers/serial_connect_write_read_event.jpg b/assets/img/faq/serialport/serial_connect_write_read_event.jpg similarity index 100% rename from assets/img/faq/how_can_i_test_the_serial_port_connection_between_two_computers/serial_connect_write_read_event.jpg rename to assets/img/faq/serialport/serial_connect_write_read_event.jpg diff --git a/assets/img/faq/how_can_i_test_the_serial_port_connection_between_two_computers/serial_connect_write_read_matlab_serial.jpg b/assets/img/faq/serialport/serial_connect_write_read_matlab_serial.jpg similarity index 100% rename from assets/img/faq/how_can_i_test_the_serial_port_connection_between_two_computers/serial_connect_write_read_matlab_serial.jpg rename to assets/img/faq/serialport/serial_connect_write_read_matlab_serial.jpg diff --git a/assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/Cronenberg.png b/assets/img/faq/sourcemodel_deformation/Cronenberg.png similarity index 100% rename from assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/Cronenberg.png rename to assets/img/faq/sourcemodel_deformation/Cronenberg.png diff --git a/assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/bad_mri.png b/assets/img/faq/sourcemodel_deformation/bad_mri.png similarity index 100% rename from assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/bad_mri.png rename to assets/img/faq/sourcemodel_deformation/bad_mri.png diff --git a/assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/fixed_mri.png b/assets/img/faq/sourcemodel_deformation/fixed_mri.png similarity index 100% rename from assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/fixed_mri.png rename to assets/img/faq/sourcemodel_deformation/fixed_mri.png diff --git a/assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/sourcespace.png b/assets/img/faq/sourcemodel_deformation/sourcespace.png similarity index 100% rename from assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/sourcespace.png rename to assets/img/faq/sourcemodel_deformation/sourcespace.png diff --git a/assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/sourcespace_fixed.png b/assets/img/faq/sourcemodel_deformation/sourcespace_fixed.png similarity index 100% rename from assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/sourcespace_fixed.png rename to assets/img/faq/sourcemodel_deformation/sourcespace_fixed.png diff --git a/assets/img/faq/how_can_i_map_source_locations_between_two_different_representations/atlas_afni_brainweb_sourcespace.png b/assets/img/faq/sourcerecon_atlas/atlas_afni_brainweb_sourcespace.png similarity index 100% rename from assets/img/faq/how_can_i_map_source_locations_between_two_different_representations/atlas_afni_brainweb_sourcespace.png rename to assets/img/faq/sourcerecon_atlas/atlas_afni_brainweb_sourcespace.png diff --git a/assets/img/faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed/singleshelldipolelocations.png b/assets/img/faq/sourcerecon_outside/singleshelldipolelocations.png similarity index 100% rename from assets/img/faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed/singleshelldipolelocations.png rename to assets/img/faq/sourcerecon_outside/singleshelldipolelocations.png diff --git a/assets/img/faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed/singlespheredipolelocations.png b/assets/img/faq/sourcerecon_outside/singlespheredipolelocations.png similarity index 100% rename from assets/img/faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed/singlespheredipolelocations.png rename to assets/img/faq/sourcerecon_outside/singlespheredipolelocations.png diff --git a/assets/img/faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed/grid_resolution_high.png b/assets/img/faq/sourcerecon_rim/grid_resolution_high.png similarity index 100% rename from assets/img/faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed/grid_resolution_high.png rename to assets/img/faq/sourcerecon_rim/grid_resolution_high.png diff --git a/assets/img/faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed/grid_resolution_low.png b/assets/img/faq/sourcerecon_rim/grid_resolution_low.png similarity index 100% rename from assets/img/faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed/grid_resolution_low.png rename to assets/img/faq/sourcerecon_rim/grid_resolution_low.png diff --git a/assets/img/faq/why_does_my_tfr_look_strange/strangetfr1.png b/assets/img/faq/tfr_strangedemean/strangetfr1.png similarity index 100% rename from assets/img/faq/why_does_my_tfr_look_strange/strangetfr1.png rename to assets/img/faq/tfr_strangedemean/strangetfr1.png diff --git a/assets/img/faq/why_does_my_tfr_look_strange/strangetfr2.png b/assets/img/faq/tfr_strangedemean/strangetfr2.png similarity index 100% rename from assets/img/faq/why_does_my_tfr_look_strange/strangetfr2.png rename to assets/img/faq/tfr_strangedemean/strangetfr2.png diff --git a/assets/img/faq/why_does_my_tfr_look_strange_part_ii/strangetfr3.png b/assets/img/faq/tfr_strangedetrend/strangetfr3.png similarity index 100% rename from assets/img/faq/why_does_my_tfr_look_strange_part_ii/strangetfr3.png rename to assets/img/faq/tfr_strangedetrend/strangetfr3.png diff --git a/assets/img/faq/why_does_my_tfr_look_strange_part_ii/strangetfr4.png b/assets/img/faq/tfr_strangedetrend/strangetfr4.png similarity index 100% rename from assets/img/faq/why_does_my_tfr_look_strange_part_ii/strangetfr4.png rename to assets/img/faq/tfr_strangedetrend/strangetfr4.png diff --git a/assets/img/getting_started/limo/herarchical_analysis.png b/assets/img/getting_started/limo/hierarchical_analysis.png similarity index 100% rename from assets/img/getting_started/limo/herarchical_analysis.png rename to assets/img/getting_started/limo/hierarchical_analysis.png diff --git a/assets/img/workshop/madrid2019/tutorial_freq/tfr_pipelinenew.png b/assets/img/workshop/madrid2019/tutorial_freq/tfr_pipelinenew.png new file mode 100644 index 000000000..b43b7013c Binary files /dev/null and b/assets/img/workshop/madrid2019/tutorial_freq/tfr_pipelinenew.png differ diff --git a/assets/img/workshop/madrid2019/tutorial_freq/tfrtiles.png b/assets/img/workshop/madrid2019/tutorial_freq/tfrtiles.png new file mode 100644 index 000000000..048b47eea Binary files /dev/null and b/assets/img/workshop/madrid2019/tutorial_freq/tfrtiles.png differ diff --git a/assets/img/workshop/oxford2019/sensor_analysis_plusminus/analysispipeline_sensor_analysis.png b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/analysispipeline_sensor_analysis.png new file mode 100644 index 000000000..83c208aea Binary files /dev/null and b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/analysispipeline_sensor_analysis.png differ diff --git a/assets/img/workshop/oxford2019/sensor_analysis_plusminus/design.png b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/design.png new file mode 100644 index 000000000..643c88098 Binary files /dev/null and b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/design.png differ diff --git a/assets/img/workshop/oxford2019/sensor_analysis_plusminus/figurepipeline.png b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/figurepipeline.png new file mode 100644 index 000000000..424889f13 Binary files /dev/null and b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/figurepipeline.png differ diff --git a/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multipletrials.png b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multipletrials.png new file mode 100644 index 000000000..67f6708e1 Binary files /dev/null and b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multipletrials.png differ diff --git a/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiploter.png b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiploter.png new file mode 100644 index 000000000..071839411 Binary files /dev/null and b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiploter.png differ diff --git a/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiploter_interactive.png b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiploter_interactive.png new file mode 100644 index 000000000..d42cb560e Binary files /dev/null and b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiploter_interactive.png differ diff --git a/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiplottfr.png b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiplottfr.png new file mode 100644 index 000000000..d15cbba4f Binary files /dev/null and b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiplottfr.png differ diff --git a/assets/img/workshop/oxford2019/sensor_analysis_plusminus/singleploter.png b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/singleploter.png new file mode 100644 index 000000000..4e845af41 Binary files /dev/null and b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/singleploter.png differ diff --git a/assets/img/workshop/oxford2019/sensor_analysis_plusminus/tfrtiles.png b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/tfrtiles.png new file mode 100644 index 000000000..048b47eea Binary files /dev/null and b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/tfrtiles.png differ diff --git a/assets/img/workshop/oxford2019/sensor_analysis_plusminus/topoploter.png b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/topoploter.png new file mode 100644 index 000000000..cfc55212f Binary files /dev/null and b/assets/img/workshop/oxford2019/sensor_analysis_plusminus/topoploter.png differ diff --git a/development/project/design.md b/development/project/design.md index 93b5b82e4..56075d8e5 100644 --- a/development/project/design.md +++ b/development/project/design.md @@ -1,5 +1,5 @@ --- -title: Explain how to create cfg.design for ft_statistics +title: Explain how to create cfg.design for ft_xxxstatistics --- {% include /shared/development/warning.md %} @@ -10,14 +10,13 @@ cfg.design as input into ft_statistics (freq, timelock, or source) should be des M is variable length. Along with cfg.design, the other options cfg.ivar, cfg.uvar, cfg.wvar, and cfg.cvar may also need to be specified. They are an index (indices) into which row(s) of the cfg.design correspond to 'independent variables', 'units of observation', 'within-block variables' and 'control variables', respectively. -Not all are needed: see statistics\_\*.m for what vectors it may include. +Not all are needed: see statistics_xxx_.m for what vectors it may include. -See https://www.fieldtriptoolbox.org/walkthrough#non-paired_comparison and https://www.fieldtriptoolbox.org/walkthrough#paired_comparison for examples on ivar and uvar. -and https://www.fieldtriptoolbox.org/development/statistics for uvar. +See https://www.fieldtriptoolbox.org/walkthrough#non-paired_comparison and https://www.fieldtriptoolbox.org/walkthrough#paired_comparison for examples on ivar and uvar, and https://www.fieldtriptoolbox.org/development/statistics for uvar. Is there any explanation on the website for more on uvar and wvar? (Seems it is all on the email discussion list specific to people's questions). -##### links to already existing pages with some mention of design matrix +## links to already existing pages with some mention of design matrix - https://www.fieldtriptoolbox.org/walkthrough - https://www.fieldtriptoolbox.org/getting_started/biosemi @@ -31,16 +30,13 @@ Is there any explanation on the website for more on uvar and wvar? (Seems it is - https://www.fieldtriptoolbox.org/development/statistics - https://www.fieldtriptoolbox.org/development/multivariate -##### Hierarchy of functions +## Hierarchy of functions (figure/diagram helpful https://www.fieldtriptoolbox.org/development/statistics) -User calls ft\_\*statistics (freq, timelock, or source) +User calls ft_xxxstatistics (freq, timelock, or source) with cfg.method=xxx as different methods for calculating probability of null hypothesis, will call function: statistics_xxx. - cfg.method: different methods for calculating probability of null hypothesis - will call function: statistics_(cfg.method) - -however, in ft_sourcestatistics, instead statistics(cfg.method) is called, or statistics_wrapper if no method specified. +However, in ft_sourcestatistics, instead statistics_xxx is called, or statistics_wrapper if no method specified. statistics_montecarlo.m (only) calls resampledesign.m diff --git a/development/testing.md b/development/testing.md index 488a36aaa..49652080e 100644 --- a/development/testing.md +++ b/development/testing.md @@ -117,8 +117,8 @@ For example, let's say you made a modification to the **[ft_preprocessing](/refe % continue with the ones that specify the WALLTIME, MEG, DATA and DEPENDENCY filtered_test = test(~skip,:); -You can then select the tests that for example depend on **[ft_preprocessing](/ft_preprocessing)**. - +You can then select the tests that for example depend on **[ft_preprocessing](/reference/ft_preprocessing)**. + keepRows = contains(filtered_test.dependency, 'ft_preprocessing'); filtered_test = filtered_test(keepRows, :); @@ -171,7 +171,7 @@ To link related scripts to background information on issues, please first file a **Method C**: If that is also not possible, the result of the algorithm on a particular real-world dataset has to be interpreted as being correct, and that solution should be reused as reference solution (i.e. regression testing). For example, if a function calculates the [forward solution](https://www.fieldtriptoolbox.org/tutorial/headmodel_meg/) for a certain subject then it should be tested against a reference solution, which could be the forward solution of a subject in MNI coordinates. -Tests that need to load test data should include **[dccnpath](/utilities/dccnpath)** to ensure that every user has the correct path to the test data. This function takes as _input_ the path to where the file is located on DCCN central storage and compute cluster; the _output_ is the corresponding path to the file on your local computer. Publicly available data is downloaded automatically from the [download server](https://download.fieldtriptoolbox.org/). +Tests that need to load test data should include **[dccnpath](/reference/utilities/dccnpath)** to ensure that every user has the correct path to the test data. This function takes as _input_ the path to where the file is located on DCCN central storage and compute cluster; the _output_ is the corresponding path to the file on your local computer. Publicly available data is downloaded automatically from the [download server](https://download.fieldtriptoolbox.org/). When you create a new test script, you should always include a _list of requirements and dependencies_ at the beginning of the script. For instance: diff --git a/faq.md b/faq.md index 89ee2bdb0..17cbe621c 100644 --- a/faq.md +++ b/faq.md @@ -13,225 +13,226 @@ See also the [tutorials](/tutorial) and [example scripts](/example). ## Reading and preprocessing data -- [How can I use the databrowser?](/faq/how_can_i_use_the_databrowser) -- [How can I inspect the electrode impedances of my data?](/faq/how_can_i_inspect_the_electrode_impedances_of_my_data) -- [Should I rereference my EEG data prior to, or after ICA?](/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal) -- [I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore?](/faq/i_used_to_work_with_trl-matrices_that_have_more_than_3_columns._why_is_this_not_supported_anymore) +- [How can I use the databrowser?](/faq/databrowser) +- [How can I inspect the electrode impedances of my data?](/faq/impedancecheck) +- [Should I rereference my EEG data prior to, or after ICA?](/faq/ica_rereference) +- [I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore?](/faq/trialinfo_trl) - [Why should I set continuous to yes for CTF data?](/faq/continuous) ### Specific data formats -- [How can I read EGI mff data without the JVM?](/faq/how_can_i_read_egi_mff_data_without_the_jvm) -- [How can I read all channels from an EDF file that contains multiple sampling rates?](/faq/how_can_i_read_all_channels_from_an_edf_file_that_contains_multiple_sampling_rates) -- [How does the CTF higher-order gradiometer work?](/faq/how_does_the_ctf_higher-order_gradiometer_work) -- [How can I extend the reading functions with a new dataformat?](/faq/how_can_i_extend_the_reading_functions_with_a_new_dataformat) -- [I have problems reading in neuroscan .cnt files. How can I fix this?](/faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this) -- [Why are the fileio functions stateless, does the fseek not make them very slow?](/faq/why_are_the_fileio_functions_stateless_does_the_fseek_not_make_them_very_slow) -- [How can I import my own dataformat?](/faq/how_can_i_import_my_own_dataformat) +- [How can I read EGI mff data without the JVM?](/faq/egi_nojvm) +- [How can I read all channels from an EDF file that contains multiple sampling rates?](/faq/edf2fieldtrip) +- [How does the CTF higher-order gradiometer work?](/faq/ctf_syntheticgradient) +- [How can I extend the reading functions with a new dataformat?](/faq/fileio_dataformat) +- [I have problems reading in neuroscan .cnt files. How can I fix this?](/faq/neuroscan) +- [Why are the fileio functions stateless, does the fseek not make them very slow?](/faq/fileio_stateless) +- [How can I import my own dataformat?](/faq/dataformat_own) - [How can I deal with a discontinuous Neuralynx recording?](/faq/discontinuous_neuralynx) -- [How can I fix a corrupt CTF meg4 data file?](/faq/how_can_i_fix_a_corrupt_ctf_meg4_data_file) -- [How can I fix a corrupt CTF res4 header file?](/faq/how_can_i_fix_a_corrupt_ctf_res4_header_file) -- [How can I read corrupted (unsaved) CTF data?](/faq/how_can_i_read_corrupted_unsaved_ctf_data) -- [I am having problems reading the CTF .hc headcoordinates file](/faq/i_am_having_problems_reading_the_ctf_.hc_headcoordinates_file) +- [How can I fix a corrupt CTF meg4 data file?](/faq/ctf_fixmeg4) +- [How can I fix a corrupt CTF res4 header file?](/faq/ctf_fixres4) +- [How can I read corrupted (unsaved) CTF data?](/faq/ctf_readcorrupted) +- [I am having problems reading the CTF .hc headcoordinates file](/faq/ctf_fixhc) ### Data handling -- [Reading is slow, can I write my raw data to a more efficient file format?](/faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format) +- [Reading is slow, can I write my raw data to a more efficient file format?](/faq/writedata_matbin) - [What dataformats are supported?](/faq/dataformat) - [How can I append the files of two separate recordings?](/faq/append_files) -- [How can I convert one dataformat into an other?](/faq/how_can_i_convert_one_dataformat_into_an_other) -- [How can I merge two datasets that were acquired simultaneously with different amplifiers?](/faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers) -- [How can I preprocess a dataset that is too large to fit into memory?](/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory) +- [How can I convert one dataformat into another?](/faq/convert_dataformat) +- [How can I merge two datasets that were acquired simultaneously with different amplifiers?](/faq/mergedata) +- [How can I preprocess a dataset that is too large to fit into memory?](/faq/preproc_downsample) - [How can I rename channels in my data structure?](/faq?rename_channels) ### Trials, triggers and events - [How can I check or decipher the sequence of triggers in my data?](/faq/triggers) -- [How can I find out what eventvalues and eventtypes there are in my data?](/faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data) -- [How can I process continuous data without triggers?](/faq/how_can_i_process_continuous_data_without_triggers) -- [How can I transform trigger values from bits to decimal representation with a trialfun?](/faq/how_can_i_transform_trigger_values_from_bits_to_decimal_representation_with_a_trialfun) -- [Is it possible to keep track of trial-specific information in my FieldTrip analysis pipeline?](/faq/is_it_possible_to_keep_track_of_trial-specific_information_in_my_fieldtrip_analysis_pipeline) +- [How can I find out what eventvalues and eventtypes there are in my data?](/faq/inspect_events) +- [How can I process continuous data without triggers?](/faq/preproc_continuous) +- [How can I transform trigger values from bits to decimal representation with a trialfun?](/faq/trialfun_bit2decimal) +- [Is it possible to keep track of trial-specific information in my FieldTrip analysis pipeline?](/faq/trialinfo) ### Artifacts -- [What kind of filters can I apply to my data?](/faq/what_kind_of_filters_can_i_apply_to_my_data) +- [What kind of filters can I apply to my data?](/faq/preproc_filtertypes) - [Do I need to resample my data, and if so, how is this to be done?](/faq/resampling_lowpassfilter) -- [I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that?](/faq/i_used_ica_on_my_meg_data_from_before_2012_and_now_fieldtrip_crashes_why_is_that) -- [Why does my ICA output contain complex numbers?](/faq/why_does_my_ica_output_contain_complex_numbers) -- [How can I consistently represent artifacts in my data?](/faq/how_can_i_consistently_represent_artifacts_in_my_data) -- [How can I interpret the different types of padding that I find when dealing with artifacts?](/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts) -- [How does the filter padding in preprocessing work?](/faq/how_does_the_filter_padding_in_preprocessing_work) -- [Why is there a residual 50Hz line-noise component after applying a DFT filter?](/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter) +- [I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that?](/faq/ica_crash) +- [Why does my ICA output contain complex numbers?](/faq/ica_complexvalues) +- [How can I consistently represent artifacts in my data?](/faq/artifact_representation) +- [How can I interpret the different types of padding that I find when dealing with artifacts?](/faq/artifact_padding) +- [How does the filter padding in preprocessing work?](/faq/preproc_padding) +- [Why is there a residual 50Hz line-noise component after applying a DFT filter?](/faq/dftfilter_residual) ## Spectral analysis - [How can I compute inter-trial coherence?](/faq/itc) -- [How can I do time-frequency analysis on continuous data?](/faq/how_can_i_do_time-frequency_analysis_on_continuous_data) +- [How can I do time-frequency analysis on continuous data?](/faq/tfr_continuous) - [How does mtmconvol work?](/faq/mtmconvol) -- [How to interpret the sign of the phase slope index?](/faq/how_to_interpret_the_sign_of_the_phase_slope_index) -- [In what way can frequency domain data be represented in FieldTrip?](/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip) -- [What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'](/faq/what_convention_is_used_to_define_absolute_phase_in_mtmconvol_wavelet_and_mtmfft) -- [What does "padding not sufficient for requested frequency resolution" mean?](/faq/what_does_padding_not_sufficient_for_requested_frequency_resolution_mean) -- [What is the difference between coherence and coherency?](/faq/what_is_the_difference_between_coherence_and_coherency) -- [Why am I not getting exact integer frequencies?](/faq/why_am_i_not_getting_exact_integer_frequencies) -- [Why does my TFR contain NaNs?](/faq/why_does_my_tfr_contain_nans) -- [Why does my TFR look strange (part I, demeaning)?](/faq/why_does_my_tfr_look_strange) -- [Why does my TFR look strange (part II, detrending)?](/faq/why_does_my_tfr_look_strange_part_ii) +- [How to interpret the sign of the phase slope index?](/faq/phaseslopeindex) +- [In what way can frequency domain data be represented in FieldTrip?](/faq/datatype_freq) +- [What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'](/faq/freqanalysis_phasedefinition) +- [What does "padding not sufficient for requested frequency resolution" mean?](/faq/freqanalysis_paddinginsufficient) +- [What is the difference between coherence and coherency?](/faq/coherence_coherency) +- [Why am I not getting exact integer frequencies?](/faq/freqanalysis_foinoninteger) +- [Why does my TFR contain NaNs?](/faq/tfr_nans) +- [Why does my TFR look strange (part I, demeaning)?](/faq/tfr_strangedemean) +- [Why does my TFR look strange (part II, detrending)?](/faq/tfr_strangedetrend) - [Why is the largest peak in the spectrum at the frequency which is 1/segment length?](/faq/why_largest_peak_spectrum) -- [Why does my output.freq not match my cfg.foi when using 'mtmconvol' in ft_freqanalyis?](/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmconvol_in_ft_freqanalyis) -- [Why does my output.freq not match my cfg.foi when using 'mtmfft' in ft_freqanalyis?](/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmfft_in_ft_freqanalyis) -- [Why does my output.freq not match my cfg.foi when using 'wavelet' (formerly 'wltconvol') in ft_freqanalyis?](/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis) +- [Why does my output.freq not match my cfg.foi when using 'mtmconvol' in ft_freqanalysis?](/faq/freqanalysis_foimismatchmtmconvol) +- [Why does my output.freq not match my cfg.foi when using 'mtmfft' in ft_freqanalysis?](/faq/freqanalysis_foimismatchmtmfft) +- [Why does my output.freq not match my cfg.foi when using 'wavelet' (formerly 'wltconvol') in ft_freqanalysis?](/faq/freqanalysis_foimismatchwavelet) - [Does it make sense to subtract the ERP prior to time frequency analysis, to distinguish evoked from induced power?](/faq/evoked_vs_induced) ## Source reconstruction -- [Can I do combined EEG and MEG source reconstruction?](/faq/can_i_do_combined_eeg_and_meg_source_reconstruction) -- [Can I restrict the source reconstruction to the grey matter?](/faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter) -- [How are electrodes, magnetometers or gradiometers described?](/faq/how_are_electrodes_magnetometers_or_gradiometers_described) -- [How are the LPA and RPA points defined?](/faq/how_are_the_lpa_and_rpa_points_defined) +- [Can I do combined EEG and MEG source reconstruction?](/faq/sourcerecon_meeg) +- [Can I restrict the source reconstruction to the grey matter?](/faq/sourcerecon_greymatter) +- [How are electrodes, magnetometers or gradiometers described?](/faq/sensors_definition) +- [How are the LPA and RPA points defined?](/faq/anat_landmarks) - [How are the different head and MRI coordinate systems defined?](/faq/coordsys) -- [How can I check whether the grid that I have is aligned to the segmented volume and to the sensor gradiometer?](/faq/how_can_i_check_whether_the_grid_that_i_have_is_aligned_to_the_segmented_volume_and_to_the_sensor_gradiometer) -- [How can I convert an anatomical mri from DICOM into CTF format?](/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format) -- [How can I determine the anatomical label of a source or electrode?](/faq/how_can_i_determine_the_anatomical_label_of_a_source) -- [How can I fine-tune my BEM volume conduction model?](/faq/how_can_i_fine-tune_my_bem_volume_conduction_model) -- [How can I map source locations onto an anatomical label in an atlas?](/faq/how_can_i_map_source_locations_between_two_different_representations) -- [How can I visualize the different geometrical objects that are needed for forward and inverse computations?](/faq/how_can_i_visualize_the_different_geometrical_objects_that_are_needed_for_forward_and_inverse_computations) -- [How do I install the OpenMEEG binaries?](/faq/how_do_i_install_the_openmeeg_binaries) +- [How can I check whether the grid that I have is aligned to the segmented volume and to the sensor gradiometer?](/faq/sourcerecon_checkalignment) +- [How can I convert an anatomical mri from DICOM into CTF format?](/faq/anat_dicom2ctf) +- [How can I determine the anatomical label of a source or electrode?](/faq/label_lookup) +- [How can I fine-tune my BEM volume conduction model?](/faq/bem_finetune) +- [How can I map source locations onto an anatomical label in an atlas?](/faq/sourcerecon_atlas) +- [How can I visualize the different geometrical objects that are needed for forward and inverse computations?](/faq/inspect_geometries) +- [How do I install the OpenMEEG binaries?](/faq/openmeeg) - [How do homogenous coordinate transformation matrices work?](/faq/homogenous) -- [How is anatomical, functional or statistical "volume data" described?](/faq/how_is_anatomical_functional_or_statistical_volume_data_described) +- [How is anatomical, functional or statistical "volume data" described?](/faq/datatype_volume) - [How should I specify the fiducials?](/faq/fiducial) -- [How to change the MRI orientation, the voxel size or the field-of-view?](/faq/how_change_mri_orientation_size_fov) -- [How to coregister an anatomical MRI with the gradiometer or electrode positions?](/faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions) -- [Is it good or bad to have dipole locations outside of the brain for which the source reconstruction is computed?](/faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed) -- [Is it important to have accurate measurements of electrode locations for EEG source reconstruction?](/faq/is_it_important_to_have_accurate_measurements_of_electrode_locations_for_eeg_source_reconstruction) -- [My MRI is upside down, is this a problem?](/faq/my_mri_is_upside_down_is_this_a_problem) +- [How to change the MRI orientation, the voxel size or the field-of-view?](/faq/anat_reslice) +- [How to coregister an anatomical MRI with the gradiometer or electrode positions?](/faq/anat_coreg) +- [Is it good or bad to have dipole locations outside of the brain for which the source reconstruction is computed?](/faq/sourcerecon_outside) +- [Is it important to have accurate measurements of electrode locations for EEG source reconstruction?](/faq/sensors_accuracy) +- [My MRI is upside down, is this a problem?](/faq/anat_upsidedown) - [Should I use a Polhemus or a Structure Sensor to record electrode positions?](/faq/structuresensor) -- [What is the conductivity of the brain, CSF, skull and skin tissue?](/faq/what_is_the_conductivity_of_the_brain_csf_skull_and_skin_tissue) +- [What is the conductivity of the brain, CSF, skull and skin tissue?](/faq/conductivity_defaults) - [What is the difference between the ACPC, MNI, SPM and TAL coordinate systems?](/faq/acpc) - [What material is used for the flexible MEG headcasts?](/faq/headcast) -- [What kind of volume conduction models are implemented?](/faq/what_kind_of_volume_conduction_models_are_implemented) -- [Where can I find the dipoli command-line executable?](/faq/where_can_i_find_the_dipoli_command-line_executable) +- [What kind of volume conduction models are implemented?](/faq/datatype_headmodel) +- [Where can I find the dipoli command-line executable?](/faq/dipoli_filelocation) - [Where is the anterior commissure?](/faq/anterior_commissure) -- [Why is there a rim around the brain for which the source reconstruction is not computed?](/faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed) -- [Why is the source model deformed or incorrectly aligned after warping template?](/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template) -- [Why should I use an average reference for EEG source reconstruction?](/faq/why_should_i_use_an_average_reference_for_eeg_source_reconstruction) -- [Why does my EEG headmodel look funny?](/faq/why_does_my_eegheadmodel_look_funny) +- [Why is there a rim around the brain for which the source reconstruction is not computed?](/faq/sourcerecon_rim) +- [Why is the source model deformed or incorrectly aligned after warping template?](/faq/sourcemodel_deformation) +- [Why should I use an average reference for EEG source reconstruction?](/faq/sourcerecon_avgref) +- [Why does my EEG headmodel look funny?](/faq/headmodel_meshingproblem) ## Statistical analysis -- [How NOT to interpret results from a cluster-based permutation test?](/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test) -- [How can I define neighbouring sensors?](/faq/how_can_i_define_neighbouring_sensors) -- [How can I determine the onset of an effect?](/faq/how_can_i_determine_the_onset_of_an_effect) -- [How can I test an interaction effect using cluster-based permutation tests?](/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests) -- [Should I use t or F values for cluster-based permutation tests?](/faq/should_I_use_t_or_F_values_for_cluster-based_permutation_tests) -- [How can I test for correlations between neuronal data and quantitative stimulus and behavioural variables?](/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables) -- [How can I test whether a behavioral measure is phasic?](/faq/how_can_i_test_whether_a_behavioral_measure_is_phasic) -- [How can I use the ivar, uvar, wvar and cvar options to precisely control the permutations?](/faq/how_can_i_use_the_ivar_uvar_wvar_and_cvar_options_to_precisely_control_the_permutations) -- [How does ft_prepare_neighbours work?](/faq/how_does_ft_prepare_neighbours_work) -- [What is the idea behind statistical inference at the second-level?](/faq/what_is_the_idea_behind_statistical_inference_at_the_second-level) -- [Why are there multiple neighbour templates for the NeuroMag306 system?](/faq/why_are_there_multiple_neighbour_templates_for_the_neuromag306_system) -- [Why should I use the cfg.correcttail option when using statistics_montecarlo?](/faq/why_should_i_use_the_cfg.correcttail_option_when_using_statistics_montecarlo) +- [How NOT to interpret results from a cluster-based permutation test?](/faq/clusterstats_interpretation) +- [How can I define neighbouring sensors?](/faq/sensors_neighbours) +- [How can I determine the onset of an effect?](/faq/effectonset) +- [How can I test an interaction effect using cluster-based permutation tests?](/faq/clusterstats_interaction) +- [Should I use t or F values for cluster-based permutation tests?](/faq/clusterstats_teststatistic) +- [How can I test for correlations between neuronal data and quantitative stimulus and behavioural variables?](/faq/behavior_signalcorrelation) +- [How can I test whether a behavioral measure is phasic?](/faq/behavior_cosinefit) +- [How can I use the ivar, uvar, wvar and cvar options to precisely control the permutations?](/faq/clusterstats_iuwcvar) +- [How does ft_prepare_neighbours work?](/faq/neighbours_prepare) +- [What is the idea behind statistical inference at the second-level?](/faq/statistics_secondlevel) +- [Why are there multiple neighbour templates for the NeuroMag306 system?](/faq/neighbours_neuromag) +- [Why should I use the cfg.correcttail option when using statistics_montecarlo?](/faq/clusterstats_correcttail) ## Plotting and visualization - [How can I play back EEG/MEG and synchronous audio or video?](/faq/audiovideo) -- [How can I visualize a 'localspheres' volume conductor model?](/faq/how_can_i_visualize_a_localspheres_volume_conductor_model) -- [How do I construct a layout file for the plotting functions?](/faq/how_do_i_construct_a_layout_file_for_the_plotting_functions) -- [I am getting strange artifacts in figures that use opacity](/faq/i_am_getting_strange_artifacts_in_figures_that_use_opacity) -- [I am having problems printing figures that use opacity](/faq/i_am_having_problems_printing_figures_that_use_opacity) -- [What are the different Neuromag and Yokogawa layouts good for?](/faq/what_are_the_different_neuromag_and_yokogawa_layouts_good_for) -- [What is a good way to save images for later processing in other software?](/faq/what_is_a_good_way_to_save_images_for_later_processing_in_other_software) -- [What is the format of the layout file, which is used for plotting?](/faq/what_is_the_format_of_the_layout_file_which_is_used_for_plotting) -- [What is the plotting convention for anatomical MRIs?](/faq/what_is_the_plotting_convention_for_anatomical_mris) -- [Why does my anatomical MRI show upside-down when plotting it with ft_sourceplot?](/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot) +- [How can I visualize a 'localspheres' volume conductor model?](/faq/headmodel_localspheres) +- [How do I construct a layout file for the plotting functions?](/faq/layout_creation) +- [I am getting strange artifacts in figures that use opacity](/faq/opacityrendering) +- [I am having problems printing figures that use opacity](/faq/figure_opacity) +- [What are the different Neuromag and Yokogawa layouts good for?](/faq/layout_magandgrad) +- [What is a good way to save images for later processing in other software?](/faq/figure_export) +- [What is the format of the layout file, which is used for plotting?](/faq/layout_fileformat) +- [What is the plotting convention for anatomical MRIs?](/faq/anat_plottingconvention) +- [Why does my anatomical MRI show upside-down when plotting it with ft_sourceplot?](/faq/anat_upsidedownplotting) - [Which colormaps are supported?](/faq/colormap) ## Experimental questions -- [How can I change the head localization in a CTF dataset?](/faq/how_can_i_change_the_head_localization_in_a_ctf_dataset) -- [How can I monitor a subject's head position during a MEG session?](/faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session) -- [How can I test the serial port connection between two computers?](/faq/how_can_i_test_the_serial_port_connection_between_two_computers) -- [How can I use my MacBook Pro for stimulus presentation in the MEG lab?](/faq/how_can_i_use_my_macbook_pro_for_stimulus_presentation_in_the_meg_lab) -- [How can I visualize the Neuromag head position indicator coils?](/faq/how_can_i_visualize_the_neuromag_head_position_indicator_coils) +- [How can I change the head localization in a CTF dataset?](/faq/ctf_changeheadloc) +- [How can I monitor a subject's head position during a MEG session?](/faq/headlocalizer) +- [How can I test the serial port connection between two computers?](/faq/serialport) +- [How can I use my MacBook Pro for stimulus presentation in the MEG lab?](/faq/psychtoolbox_macbook) +- [How can I visualize the Neuromag head position indicator coils?](/faq/neuromag_hpi) ## Realtime data streaming and analysis -- [Does the FieldTrip realtime buffer only work with MATLAB?](/faq/does_the_fieldtrip_realtime_buffer_only_work_with_matlab) -- [How fast is the FieldTrip buffer for realtime data streaming?](/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming) -- [How should I get started with the FieldTrip realtime buffer?](/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer) +- [Does the FieldTrip realtime buffer only work with MATLAB?](/faq/fieldtripbuffer) +- [How fast is the FieldTrip buffer for realtime data streaming?](/faq/fieldtripbuffer_speed) +- [How should I get started with the FieldTrip realtime buffer?](/faq/fieldtripbuffer_gettingstarted) ## Distributed computing -- [What are the different approaches I can take for distributed computing?](/faq/what_are_the_different_approaches_i_can_take_for_distributed_computing) +- [What are the different approaches I can take for distributed computing?](/faq/distributed_computing) ### Distributed computing with the MATLAB distributed computing toolbox -- [How to get started with the MATLAB distributed computing toolbox?](/faq/how_to_get_started_with_the_matlab_distributed_computing_toolbox) +- [How to get started with the MATLAB distributed computing toolbox?](/faq/distributed_matlab) ### Distributed computing with fieldtrip/qsub on a HPC cluster -- [How to compile MATLAB code into stand-alone executables?](/faq/how_to_compile_matlab_code_into_stand-alone_executables) -- [How to get started with distributed computing using qsub?](/faq/how_to_get_started_with_distributed_computing_using_qsub) +- [How to compile MATLAB code into stand-alone executables?](/faq/matlab_compile) +- [How to get started with distributed computing using qsub?](/faq/distributed_qsub) ## MATLAB questions - [Installation and setting up the path](/faq/installation) -- [Can I prevent "external" toolboxes from being added to my MATLAB path?](/faq/can_i_prevent_external_toolboxes_from_being_added_to_my_matlab_path) +- [Can I prevent "external" toolboxes from being added to my MATLAB path?](/faq/toolboxes_legacyvsexternal) - [Can I use FieldTrip without MATLAB license?](/faq/compiled) -- [Can I use Octave instead of MATLAB?](/faq/can_i_use_octave_instead_of_matlab) +- [Can I use Octave instead of MATLAB?](/faq/octave) - [How can I compile the mex files and command-line programs?](/faq/compile) -- [How can I compile the mex files on 64-bit Windows?](/faq/how_can_i_compile_the_mex_files_on_64_bit_windows) -- [How can I compile the mex files on macOS?](/faq/how_can_i_compile_the_mex_files_on_os_x) -- [How many lines of code does FieldTrip consist of?](/faq/how_many_lines_of_code_does_fieldtrip_consist_of) -- [How to select the correct SPM toolbox?](/faq/how_to_select_the_correct_spm_toolbox) -- [MATLAB complains about a missing or invalid MEX file, what should I do?](/faq/matlab_complains_about_a_missing_or_invalid_mex_file_what_should_i_do) -- [MATLAB complains that mexmaci64 cannot be opened because the developer cannot be verified](/faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified) -- [MATLAB does not see the functions in the "private" directory](/faq/matlab_does_not_see_the_functions_in_the_private_directory) -- [MATLAB version 7.3 (2006b)_crashes_when_I_try_to_do_...](/faq/matlab_version_7.3_2006b_crashes_when_i_try_to_do) -- [The databrowser crashes and destroys the whole MATLAB session, how can I resolve this?](/faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this) +- [How can I compile the mex files on 64-bit Windows?](/faq/compile_windows) +- [How can I compile the mex files on macOS?](/faq/compile_osx) +- [How many lines of code does FieldTrip consist of?](/faq/fieldtrip_codelines) +- [How to select the correct SPM toolbox?](/faq/spmversion) +- [MATLAB complains about a missing or invalid MEX file, what should I do?](/faq/matlab_mexinvalid) +- [MATLAB complains that mexmaci64 cannot be opened because the developer cannot be verified](/faq/mex_osx) +- [MATLAB does not see the functions in the "private" directory](/faq/matlab_privatefunctions) +- [MATLAB version 7.3 (2006b)_crashes_when_I_try_to_do_...](/faq/matlab_crash73) +- [The databrowser crashes and destroys the whole MATLAB session, how can I resolve this?](/faq/databrowser_crash) - [What are the MATLAB requirements for using FieldTrip?](/faq/requirements) -- [What is the relation between "events" (such as_triggers) and "trials"?](/faq/what_is_the_relation_between_events_such_as_triggers_and_trials) +- [What is the relation between "events" (such as_triggers) and "trials"?](/faq/eventsversustrials) - [Which external toolboxes are used by FieldTrip?](/faq/external) -- [Why are so many of the interesting functions in the private directories?](/faq/why_are_so_many_of_the_interesting_functions_in_the_private_directories) +- [Why are so many of the interesting functions in the private directories?](/faq/privatefunctions_why) ## Code and development questions -- [How are the various data structures defined?](/faq/how_are_the_various_data_structures_defined) -- [How can I debug my analysis script if a FieldTrip function gives an error?](/faq/how_can_i_debug_my_analysis_script_if_a_fieldtrip_function_gives_an_error) -- [How can I keep track of the changes to the code?](/faq/how_can_i_keep_track_of_the_changes_to_the_code) -- [What does a typical call to a FieldTrip function look like?](/faq/what_does_a_typical_call_to_a_fieldtrip_function_look_like) -- [Why is FieldTrip maintained in SVN and not in git?](/faq/why_is_fieldtrip_maintained_in_svn_and_not_in_git) +- [How are the various data structures defined?](/faq/datatype) +- [How can I debug my analysis script if a FieldTrip function gives an error?](/faq/matlab_debugging) +- [How can I keep track of the changes to the code?](/faq/trackchanges) +- [What does a typical call to a FieldTrip function look like?](/faq/fieldtrip_functioncall) +- [Why is FieldTrip maintained in SVN and not in git?](/faq/svnversusgit) ## Organizational questions -- [Can I get an offline version of the website documentation?](/faq/can_i_get_an_offline_version_of_the_wiki_documentation) -- [Can I use the FieldTrip logo on my poster?](/faq/can_i_use_the_fieldtrip_logo_on_my_poster) -- [How many people are subscribed to the email discussion list?](/faq/how_many_people_are_subscribed_to_the_email_discussion_list) -- [How should I refer to FieldTrip in my publication?](/faq/how_should_i_refer_to_fieldtrip_in_my_publication) -- [How should I send example data to the developers?](/faq/how_should_i_send_example_data_to_the_developers) -- [How to ask good questions to the community?](/faq/how_to_ask_good_questions_to_the_community) -- [I am having problems downloading](/faq/i_am_having_problems_downloading) -- [I am working at the Donders, should I also download FieldTrip?](/faq/i_am_working_at_the_donders_should_i_also_download_fieldtrip) -- [Which version of FieldTrip should I download?](/faq/which_version_of_fieldtrip_should_i_download) -- [Why am I not allowed to post to the discussion list?](/faq/why_am_i_not_allowed_to_post_to_the_discussion_list) -- [Why am I not receiving emails from the discussion list?](/faq/why_am_i_not_receiving_emails_from_the_discussion_list) -- [Why am I receiving warnings about too many bouncing emails?](/faq/why_am_i_receiving_warnings_about_too_many_bouncing_emails) -- [Why is FieldTrip developed separately from EEGLAB?](/faq/why_is_fieldtrip_developed_separately_from_eeglab) -- [Why is my message rejected from the email discussion list?](/faq/why_is_my_message_rejected_from_the_email_discussion_list) +- [Can I get an offline version of the website documentation?](/faq/documentation_offline) +- [Can I use the FieldTrip logo on my poster?](/faq/fieldtriplogo) +- [How many people are subscribed to the email discussion list?](/faq/emaillist_subscribers) +- [How should I refer to FieldTrip in my publication?](/faq/fieldtrip_reference) +- [How should I send example data to the developers?](/faq/datasharing) +- [How to ask good questions to the community?](/faq/emaillist_howtoask) +- [I am having problems downloading](/faq/download_ftpproblem) +- [I am working at the Donders, should I also download FieldTrip?](/faq/download_donders) +- [Which version of FieldTrip should I download?](/faq/fieldtrip_downloadversion) +- [Why am I not allowed to post to the discussion list?](/faq/emaillist_nopost) +- [Why am I not receiving emails from the discussion list?](/faq/emaillist_noreceive) +- [Why am I receiving warnings about too many bouncing emails?](/faq/emaillist_bounces) +- [Why is FieldTrip developed separately from EEGLAB?](/faq/fieldtrip_eeglab) +- [Why is my message rejected from the email discussion list?](/faq/emaillist_rejected) ## Various other questions - [Are the FieldTrip lectures available on video?](/faq/video) - [Can I map different electrode position layouts?](/faq/capmapping) -- [Can I organize my own FieldTrip workshop?](/faq/can_i_organize_my_own_workshop) -- [How can I anonymize DICOM files?](/faq/how_can_i_anonymize_dicom_files) -- [How can I anonymize a CTF dataset?](/faq/how_can_i_anonymize_a_ctf_dataset) -- [How can I anonymize data processed in FieldTrip?](/faq/how_can_i_anonymize_fieldtrip_data) -- [How can I anonymize or deidentify an anatomical MRI?](/faq/how_can_i_anonymize_an_anatomical_mri) -- [How can I convert an anatomical MRI from DICOM into CTF format?](/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format) +- [Can I organize my own FieldTrip workshop?](/faq/workshop) +- [How can I anonymize DICOM files?](/faq/anonymization_dicom) +- [How can I anonymize a CTF dataset?](/faq/anonymization_ctf) +- [How can I anonymize a brainvisino dataset?](/faq/anonymization_brainvision) +- [How can I anonymize data processed in FieldTrip?](/faq/anonymization_fieldtripdata) +- [How can I anonymize or deidentify an anatomical MRI?](/faq/anonymization_anatomical) +- [How can I convert an anatomical MRI from DICOM into CTF format?](/faq/anat_dicom2ctf) - [How can I share my MEG data?](/faq/data_sharing) -- [How do I prevent FieldTrip from printing the time and memory after each function call?](/faq/how_do_i_prevent_fieldtrip_from_printing_the_time_and_memory_after_each_function_call) -- [How should I prepare for the upcoming FieldTrip workshop?](/faq/how_should_i_prepare_for_the_upcoming_fieldtrip_workshop) +- [How do I prevent FieldTrip from printing the time and memory after each function call?](/faq/showcallinfo) +- [How should I prepare for the upcoming FieldTrip workshop?](/faq/workshop_preparation) - [How should I specify the coordinate systems in a BIDS dataset?](/faq/bids_coordsystem) - [What are the units of the data and of the derived results?](/faq/units) - [Which datasets are used in the documentation and where are they used?](/faq/datasets) diff --git a/faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions.md b/faq/anat_coreg.md similarity index 96% rename from faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions.md rename to faq/anat_coreg.md index 5956d6423..112ed3dd1 100644 --- a/faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions.md +++ b/faq/anat_coreg.md @@ -2,6 +2,8 @@ title: How to coregister an anatomical MRI with the gradiometer or electrode positions? category: faq tags: [eeg, meg, mri, headmodel, source, coordinate] +redirect_from: + - /faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions/ --- # How to coregister an anatomical MRI with the gradiometer or electrode positions? diff --git a/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format.md b/faq/anat_dicom2ctf.md similarity index 88% rename from faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format.md rename to faq/anat_dicom2ctf.md index b0f4bc665..1a4e84ec0 100644 --- a/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format.md +++ b/faq/anat_dicom2ctf.md @@ -2,6 +2,8 @@ title: How can I convert an anatomical MRI from DICOM into CTF format? category: faq tags: [mri, meg, ctf, dataformat, coordinate] +redirect_from: + - /faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/ --- # How can I convert an anatomical MRI from DICOM into CTF format? @@ -42,9 +44,9 @@ The conversion involves two steps, both using the CTF-program MRIViewer: First, The earphone of the MRI scanner has a large (~1 cm) vitamine E marker built in on the right side. Make sure to check that this marker is visible on the right side. -{% include image src="/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/vitamine_marker1.png" width="150" %} -{% include image src="/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/vitamine_marker2.png" width="150" %} -{% include image src="/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/vitamine_marker3.png" width="150" %} +{% include image src="/assets/img/faq/anat_dicom2ctf/vitamine_marker1.png" width="150" %} +{% include image src="/assets/img/faq/anat_dicom2ctf/vitamine_marker2.png" width="150" %} +{% include image src="/assets/img/faq/anat_dicom2ctf/vitamine_marker3.png" width="150" %} ### Directory structure @@ -85,9 +87,9 @@ While still in MRIViewer, perform the following action At the DCCN we use ear-molds that come in a variety of sizes to position the MEG head localiser coils just outside the left and right ear . For the MRI we use the same ear-molds, but now with small MRI markers. -{% include image src="/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/ear_molds_1.jpg" width="400" %} +{% include image src="/assets/img/faq/anat_dicom2ctf/ear_molds_1.jpg" width="400" %} -{% include image src="/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/ear_molds_2.jpg" width="400" %} +{% include image src="/assets/img/faq/anat_dicom2ctf/ear_molds_2.jpg" width="400" %} {% include markup/red %} Note that the photo above is incorrect and misleading: it shows one of the markers plugged into the earmold on the _inside_, whereas in reality they are plugged into the mold on the _outside_, facing away from the ear. The markers would actually also be too big to fit in the ear canal. @@ -97,9 +99,9 @@ In the MRI below you can see the small dot (the marker) with the yellow arrow ho On top of that, the right ear also contains a large vitamine E marker to help distinguish left and right. At the location of the nasion we don't put a marker. Below you see three slices with the right-ear marker. Note that the ear marker is the small dot in the middle of the ear shell (yellow arrow), not the large dot close to the ear lobe (red arrow; that is the vitamine E capsule to indicate the right side). -{% include image src="/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/fiducials1.png" width="150" %} -{% include image src="/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/fiducials2.png" width="150" %} -{% include image src="/assets/img/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format/fiducials3.png" width="150" %} +{% include image src="/assets/img/faq/anat_dicom2ctf/fiducials1.png" width="150" %} +{% include image src="/assets/img/faq/anat_dicom2ctf/fiducials2.png" width="150" %} +{% include image src="/assets/img/faq/anat_dicom2ctf/fiducials3.png" width="150" %} The most elegant way to identify the markers would include: diff --git a/faq/how_are_the_lpa_and_rpa_points_defined.md b/faq/anat_landmarks.md similarity index 89% rename from faq/how_are_the_lpa_and_rpa_points_defined.md rename to faq/anat_landmarks.md index 003eb55f1..420da0b9e 100644 --- a/faq/how_are_the_lpa_and_rpa_points_defined.md +++ b/faq/anat_landmarks.md @@ -2,17 +2,19 @@ title: How are the Left and Right Pre-Auricular (LPA and RPA) points defined? category: faq tags: [fiducial, mri, ctf, source, coordinate] +redirect_from: + - /faq/how_are_the_lpa_and_rpa_points_defined/ --- # How are the Left and Right Pre-Auricular (LPA and RPA) points defined? The definition of the pre-auricular point taken from is _"a point of the posterior root of the zygomatic arch lying immediately in front of the upper end of the tragus"_. The [zygomatic arch](https://en.wikipedia.org/wiki/Zygomatic_arch) or cheek bone is the skull bone in front of the ear as depicted in this figure -{% include image src="/assets/img/faq/how_are_the_lpa_and_rpa_points_defined/zygomatic_arch.png" width="200" %} +{% include image src="/assets/img/faq/anat_landmarks/zygomatic_arch.png" width="200" %} and the [tragus]() is a small backward-pointing eminence situated in front of the ear canal. -{% include image src="/assets/img/faq/how_are_the_lpa_and_rpa_points_defined/tragus.png" width="200" %} +{% include image src="/assets/img/faq/anat_landmarks/tragus.png" width="200" %} The approximate position of the pre-auricular point is indicated in the figure above by the green point. It can be palpated (i.e. felt with the finger tip) the best if the subject moves his jaw by opening and closing his or her mouth. @@ -26,9 +28,9 @@ Because of the challenge of localizing the LPA and RPA points when doing EEG or At the Donders Centre for Cognitive Neuroimaging (DCCN) in Nijmegen we use silicone ear molds with a hole in them (see below) to attach the markers: In the MEG scanner we insert a small tube into the hole (the tube is also used for auditory stimulation) and attach the MEG localizer coil to the tube. In the MRI scanner we use the same ear molds, but rather insert a custom-made marker with a small drop of vitamine E into the hole. The position thereby obtained with the MEG localizer coils is as precisely as possible reproduced in the MRI, given the movement that is allowed by the ear molds. We have various sizes of ear molds, both at the MEG and MRI scanner, and subjects should use the same size in both scanners. -{% include image src="/assets/img/faq/how_are_the_lpa_and_rpa_points_defined/ear_molds_1.jpg" width="200" %} +{% include image src="/assets/img/faq/anat_landmarks/ear_molds_1.jpg" width="200" %} -{% include image src="/assets/img/faq/how_are_the_lpa_and_rpa_points_defined/ear_molds_2.jpg" width="200" %} +{% include image src="/assets/img/faq/anat_landmarks/ear_molds_2.jpg" width="200" %} When using different fiducial locations in the MEG and the MRI, the difference in the coordinates (which can be 5-20 mm) has to be taken into account in the coregistration procedure, otherwise the source localization would suffer from the systematic coregistration error. Luckily, most research labs acquire the EEG/MEG and the MRI using the same fiducial locations. diff --git a/faq/what_is_the_plotting_convention_for_anatomical_mris.md b/faq/anat_plottingconvention.md similarity index 98% rename from faq/what_is_the_plotting_convention_for_anatomical_mris.md rename to faq/anat_plottingconvention.md index 048d882b7..9a491b1c6 100644 --- a/faq/what_is_the_plotting_convention_for_anatomical_mris.md +++ b/faq/anat_plottingconvention.md @@ -2,6 +2,8 @@ title: What is the plotting convention for anatomical MRIs? category: faq tags: [anatomical, mri] +redirect_from: + - /faq/what_is_the_plotting_convention_for_anatomical_mris/ --- # What is the plotting convention for anatomical MRIs? diff --git a/faq/how_change_mri_orientation_size_fov.md b/faq/anat_reslice.md similarity index 94% rename from faq/how_change_mri_orientation_size_fov.md rename to faq/anat_reslice.md index 2fdbf8106..c0cf4024a 100644 --- a/faq/how_change_mri_orientation_size_fov.md +++ b/faq/anat_reslice.md @@ -2,6 +2,8 @@ title: How to change the MRI orientation, the voxel size or the field-of-view? category: faq tags: [mri, volume, coordinate] +redirect_from: + - /faq/how_change_mri_orientation_size_fov/ --- # How to change the MRI orientation, the voxel size or the field-of-view? @@ -35,7 +37,7 @@ When the anatomical data is plotted, the default behavior is to plot the anatomi cfg = []; ft_sourceplot(cfg,mri) -{% include image src="/assets/img/faq/how_change_mri_orientation_size_fov/mri.png" width="400" %} +{% include image src="/assets/img/faq/anat_reslice/mri.png" width="400" %} _Figure 1. Anatomical mri plotted **without** using ft_volumereslice before plotting_ @@ -49,7 +51,7 @@ Plotting the resliced anatomical MRI results in a figure with the usually desire cfg = []; ft_sourceplot(cfg,mrirs); -{% include image src="/assets/img/faq/how_change_mri_orientation_size_fov/mrirs.png" %} +{% include image src="/assets/img/faq/anat_reslice/mrirs.png" %} _Figure 2. Plot of the anatomical mri after using ft_volumereslice_ @@ -69,6 +71,6 @@ In the figures above you can appreciate the change in the FOV by considering the The **[ft_volumereslice](/reference/ft_volumereslice)** operations, such as changing the orientation of the anatomy and changing the resolution of the voxels can be conceptually understood by looking at the figure below: -{% include image src="/assets/img/faq/how_change_mri_orientation_size_fov/reslice2.jpg" width="500" %} +{% include image src="/assets/img/faq/anat_reslice/reslice2.jpg" width="500" %} The figure shows the original volumetric slices (dotted black lines) and the desired slices (bold red). Note that the distance between the original slices is 2 cm, whereas the pixel distance within the same slice is 1 cm (black). After re-slicing (red) the voxels' dimensions are the same. You can also see that the voxels are aligned with the axes of the coordinate system to which the image was re-aligned earlier (see the black vs. red axes at the bottom of the figures). diff --git a/faq/my_mri_is_upside_down_is_this_a_problem.md b/faq/anat_upsidedown.md similarity index 93% rename from faq/my_mri_is_upside_down_is_this_a_problem.md rename to faq/anat_upsidedown.md index eaa22d478..b86e85aea 100644 --- a/faq/my_mri_is_upside_down_is_this_a_problem.md +++ b/faq/anat_upsidedown.md @@ -2,6 +2,8 @@ title: My MRI is upside down, is this a problem? category: faq tags: [mri, volume, coordinate] +redirect_from: + - /faq/my_mri_is_upside_down_is_this_a_problem/ --- # My MRI is upside down, is this a problem? @@ -12,6 +14,6 @@ The bottom line is now, that **if your anatomical volume is registered to a mean If you still find the upside-down issue problematic, you can use **[ft_volumereslice](/reference/ft_volumereslice)**. See this Frequently Asked Question about [reslicing of an MRI ](/faq/how_change_mri_orientation_size_fov) for more information. -{% include image src="/assets/img/faq/my_mri_is_upside_down_is_this_a_problem/potatomen.png" width="600" %} +{% include image src="/assets/img/faq/anat_upsidedown/potatomen.png" width="600" %} _Figure; The interpretation of the axes in the voxel coordinate system (pink) depends on how the anatomy is stored in the 'box', but the interpretation of the axes in the potato-related coordinate system (green) stays the same. This is irrespective of how the anatomy is stored in the box._ diff --git a/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot.md b/faq/anat_upsidedownplotting.md similarity index 65% rename from faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot.md rename to faq/anat_upsidedownplotting.md index c39aedadb..eb6bbc433 100644 --- a/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot.md +++ b/faq/anat_upsidedownplotting.md @@ -2,16 +2,18 @@ title: Why does my anatomical MRI show upside-down when plotting it with ft_sourceplot? category: faq tags: [anatomical, mri] +redirect_from: + - /faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot/ --- # Why does my anatomical MRI show upside-down when plotting it with ft_sourceplot? -When visualizing anatomical MRIs and source reconstructed data with **[ft_sourceplot](/reference/ft_sourceplot)**, it may happen that the image is plotted upside-down. This has to do with the way in which anatomical volumes are plotted in FieldTrip. For more information, see the frequently asked question [What is the plotting convention for anatomical MRIs?](/faq/what_is_the_plotting_convention_for_anatomical_mris). +When visualizing anatomical MRIs and source reconstructed data with **[ft_sourceplot](/reference/ft_sourceplot)**, it may happen that the image is plotted upside-down. This has to do with the way in which anatomical volumes are plotted in FieldTrip. For more information, see the frequently asked question [What is the plotting convention for anatomical MRIs?](/faq/anat_plottingconvention). -{% include image src="/assets/img/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot/upside_down_sourceplot.png" width="400" %} +{% include image src="/assets/img/faq/anat_upsidedownplotting/upside_down_sourceplot.png" width="400" %} -In itself this is **not a problem**, as explained [here](/faq/my_mri_is_upside_down_is_this_a_problem). +In itself this is **not a problem**, as explained [here](/faq/anat_upsidedown). If for aesthetic reasons you do want the figure to be plotted upside-up, you can use the **[ft_volumereslice](/reference/ft_volumereslice)** function to reslice the MRI, i.e. to interpolate the anatomy onto a new 3D grid that is aligned with the axes of the coordinate system. If you use the resliced MRI as input to **[ft_sourceinterpolate](/reference/ft_sourceinterpolate)**, the source reconstructed result will also show up as expected. -{% include image src="/assets/img/faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot/correct_sourceplot.png" width="400" %} +{% include image src="/assets/img/faq/anat_upsidedownplotting/correct_sourceplot.png" width="400" %} diff --git a/faq/how_can_i_anonymize_an_anatomical_mri.md b/faq/anonymization_anatomical.md similarity index 92% rename from faq/how_can_i_anonymize_an_anatomical_mri.md rename to faq/anonymization_anatomical.md index d6e6700a8..317141dae 100644 --- a/faq/how_can_i_anonymize_an_anatomical_mri.md +++ b/faq/anonymization_anatomical.md @@ -2,6 +2,8 @@ title: How can I anonymize or deidentify an anatomical MRI? category: faq tags: [mri, anonymize, sharing] +redirect_from: + - /faq/how_can_i_anonymize_an_anatomical_mri/ --- # How can I anonymize or deidentify an anatomical MRI? @@ -17,11 +19,11 @@ You can deface an anatomical MRI using the FieldTrip **[ft_defacevolume](/refere cfg = []; mri_anon = ft_defacevolume(cfg, mri); -{% include image src="/assets/img/faq/how_can_i_anonymize_an_anatomical_mri/defacevolume2.png" width="400" %} +{% include image src="/assets/img/faq/anonymization_anatomical/defacevolume2.png" width="400" %} You can use the standard MATLAB figure rotate button to look at the MRI from different angles. -{% include image src="/assets/img/faq/how_can_i_anonymize_an_anatomical_mri/defacevolume1.png" width="400" %} +{% include image src="/assets/img/faq/anonymization_anatomical/defacevolume1.png" width="400" %} Once you are happy with the size and position of the box, you close the figure and the function returns the defaced anatomical MRI. @@ -32,7 +34,7 @@ It is good practice to review the result of the defacing procedure using cfg = []; ft_sourceplot(cfg, mri_anon); -{% include image src="/assets/img/faq/how_can_i_anonymize_an_anatomical_mri/defacevolume3.png" width="400" %} +{% include image src="/assets/img/faq/anonymization_anatomical/defacevolume3.png" width="400" %} Subsequently you can save it to a MATLAB file or to a NIFTI file using diff --git a/faq/how_can_i_anonymize_a_brainvision_dataset.md b/faq/anonymization_brainvision.md similarity index 98% rename from faq/how_can_i_anonymize_a_brainvision_dataset.md rename to faq/anonymization_brainvision.md index ad5d71772..8540bbff6 100644 --- a/faq/how_can_i_anonymize_a_brainvision_dataset.md +++ b/faq/anonymization_brainvision.md @@ -2,6 +2,8 @@ title: How can I anonymize or deidentify a BrainVision dataset? category: faq tags: [brainvision, raw, anonymize, sharing] +redirect_from: + - /faq/how_can_i_anonymize_a_brainvision_dataset/ --- # How can I anonymize or deidentify a BrainVision dataset? diff --git a/faq/how_can_i_anonymize_a_ctf_dataset.md b/faq/anonymization_ctf.md similarity index 98% rename from faq/how_can_i_anonymize_a_ctf_dataset.md rename to faq/anonymization_ctf.md index 35ecd3000..9eccc299a 100644 --- a/faq/how_can_i_anonymize_a_ctf_dataset.md +++ b/faq/anonymization_ctf.md @@ -2,6 +2,8 @@ title: How can I anonymize or deidentify a CTF dataset? category: faq tags: [ctf, raw, anonymize, sharing] +redirect_from: + - /faq/how_can_i_anonymize_a_ctf_dataset/ --- # How can I anonymize or deidentify a CTF dataset? diff --git a/faq/how_can_i_anonymize_dicom_files.md b/faq/anonymization_dicom.md similarity index 98% rename from faq/how_can_i_anonymize_dicom_files.md rename to faq/anonymization_dicom.md index 3ecebd025..dd08286ef 100644 --- a/faq/how_can_i_anonymize_dicom_files.md +++ b/faq/anonymization_dicom.md @@ -2,6 +2,8 @@ title: How can I anonymize or deidentify DICOM files? category: faq tags: [mri, anonymize, sharing] +redirect_from: + - /faq/how_can_i_anonymize_dicom_files/ --- # How can I anonymize or deidentify DICOM files? diff --git a/faq/how_can_i_anonymize_fieldtrip_data.md b/faq/anonymization_fieldtripdata.md similarity index 98% rename from faq/how_can_i_anonymize_fieldtrip_data.md rename to faq/anonymization_fieldtripdata.md index a36a672b4..f36bf3f47 100644 --- a/faq/how_can_i_anonymize_fieldtrip_data.md +++ b/faq/anonymization_fieldtripdata.md @@ -2,6 +2,8 @@ title: How can I anonymize data processed in FieldTrip? category: faq tags: [sharing, anonymize] +redirect_from: + - /faq/how_can_i_anonymize_fieldtrip_data/ --- # How can I anonymize data processed in FieldTrip? diff --git a/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts.md b/faq/artifact_padding.md similarity index 89% rename from faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts.md rename to faq/artifact_padding.md index ecc48980e..1c3fd3426 100644 --- a/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts.md +++ b/faq/artifact_padding.md @@ -2,6 +2,8 @@ title: How can I interpret the different types of padding in FieldTrip? category: faq tags: [preprocessing, artifact, filter] +redirect_from: + - /faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts/ --- # How can I interpret the different types of padding in FieldTrip? @@ -21,9 +23,9 @@ There are different purposes for padding in the artifact detection functions: - filter padding (fig 1): zero padding **with**, to extend the data segment to prevent edge artifacts due to filtering. - artifact padding (fig 2): data padding **with**, to extend the length of a detected artifact, for example if you also want to exclude data from being analyzed in a time window following some artifact. -{% include image src="/assets/img/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts/padding_fig1.png" %} +{% include image src="/assets/img/faq/artifact_padding/padding_fig1.png" %} -{% include image src="/assets/img/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts/padding_fig2.png" %} +{% include image src="/assets/img/faq/artifact_padding/padding_fig2.png" %} See also the [automatic artifact rejection tutorial](/tutorial/automatic_artifact_rejection) for more details on the filter padding, trial padding and artifact padding. diff --git a/faq/how_can_i_consistently_represent_artifacts_in_my_data.md b/faq/artifact_representation.md similarity index 95% rename from faq/how_can_i_consistently_represent_artifacts_in_my_data.md rename to faq/artifact_representation.md index 6b38d7683..c26042b45 100644 --- a/faq/how_can_i_consistently_represent_artifacts_in_my_data.md +++ b/faq/artifact_representation.md @@ -2,6 +2,8 @@ title: How can I consistently represent artifacts in my data? category: faq tags: [preprocessing, artifact] +redirect_from: + - /faq/how_can_i_consistently_represent_artifacts_in_my_data/ --- # How can I consistently represent artifacts in my data? diff --git a/faq/how_can_i_test_whether_a_behavioral_measure_is_phasic.md b/faq/behavior_cosinefit.md similarity index 98% rename from faq/how_can_i_test_whether_a_behavioral_measure_is_phasic.md rename to faq/behavior_cosinefit.md index 912114cc7..76bb2f2ae 100644 --- a/faq/how_can_i_test_whether_a_behavioral_measure_is_phasic.md +++ b/faq/behavior_cosinefit.md @@ -2,6 +2,8 @@ title: How can I test whether a behavioral measure is phasic? category: faq tags: [statistics, freq] +redirect_from: + - /faq/how_can_i_test_whether_a_behavioral_measure_is_phasic/ --- # How can I test whether a behavioral measure is phasic? diff --git a/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables.md b/faq/behavior_signalcorrelation.md similarity index 98% rename from faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables.md rename to faq/behavior_signalcorrelation.md index 882a2c870..84959669c 100644 --- a/faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables.md +++ b/faq/behavior_signalcorrelation.md @@ -2,6 +2,8 @@ title: How can I test for correlations between neuronal data and quantitative stimulus and behavioral variables? category: faq tags: [statistics] +redirect_from: + - /faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables/ --- # How can I test for correlations between neuronal data and quantitative stimulus and behavioral variables? diff --git a/faq/how_can_i_fine-tune_my_bem_volume_conduction_model.md b/faq/bem_finetune.md similarity index 96% rename from faq/how_can_i_fine-tune_my_bem_volume_conduction_model.md rename to faq/bem_finetune.md index 826a08203..c67bfa727 100644 --- a/faq/how_can_i_fine-tune_my_bem_volume_conduction_model.md +++ b/faq/bem_finetune.md @@ -2,6 +2,8 @@ title: How can I fine-tune my BEM volume conduction model? category: faq tags: [source, headmodel] +redirect_from: + - /faq/how_can_i_fine-tune_my_bem_volume_conduction_model/ --- # How can I fine-tune my BEM volume conduction model? @@ -46,7 +48,7 @@ The MATLAB image processing toolbox includes a number of morphological operation In particular imdilate can be used to augment the volume of a closed surface (e.g., the inner skull) in order to render the other surrounding tissues (e.g., the outer skull). An example is shown below: -{% include image src="/assets/img/faq/how_can_i_fine-tune_my_bem_volume_conduction_model/wiki12.png" width="300" %} +{% include image src="/assets/img/faq/bem_finetune/wiki12.png" width="300" %} The code used to generate the figure is: @@ -56,7 +58,7 @@ The code used to generate the figure is: An example of the imfill function is given below. This is the case, for example, in which we want to fill the volume so that it constitutes a single entity. It results in being useful for triangulation, as explained in one of the techniques to obtain the outer-most surface (i.e. the skin). -{% include image src="/assets/img/faq/how_can_i_fine-tune_my_bem_volume_conduction_model/wiki34.png" width="300" %} +{% include image src="/assets/img/faq/bem_finetune/wiki34.png" width="300" %} The code used to generate the figure is: diff --git a/faq/why_should_i_use_the_cfg.correcttail_option_when_using_statistics_montecarlo.md b/faq/clusterstats_correcttail.md similarity index 95% rename from faq/why_should_i_use_the_cfg.correcttail_option_when_using_statistics_montecarlo.md rename to faq/clusterstats_correcttail.md index 77676c6af..245bb057e 100644 --- a/faq/why_should_i_use_the_cfg.correcttail_option_when_using_statistics_montecarlo.md +++ b/faq/clusterstats_correcttail.md @@ -2,6 +2,8 @@ title: Why should I use the cfg.correcttail option when using statistics_montecarlo? category: faq tags: [statistics, cluster] +redirect_from: + - /faq/why_should_i_use_the_cfg.correcttail_option_when_using_statistics_montecarlo/ --- # Why should I use the cfg.correcttail option when using statistics_montecarlo? diff --git a/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests.md b/faq/clusterstats_interaction.md similarity index 98% rename from faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests.md rename to faq/clusterstats_interaction.md index ac1b89e27..d6792854b 100644 --- a/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests.md +++ b/faq/clusterstats_interaction.md @@ -2,6 +2,8 @@ title: How to test an interaction effect using cluster-based permutation tests? category: faq tags: [statistics] +redirect_from: + - /faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests/ --- # How to test an interaction effect using cluster-based permutation tests? diff --git a/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test.md b/faq/clusterstats_interpretation.md similarity index 98% rename from faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test.md rename to faq/clusterstats_interpretation.md index a55489d05..ee8f95354 100644 --- a/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test.md +++ b/faq/clusterstats_interpretation.md @@ -2,6 +2,8 @@ title: How NOT to interpret results from a cluster-based permutation test category: faq tags: [statistics] +redirect_from: + - /faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test/ --- # How NOT to interpret results from a cluster-based permutation test diff --git a/faq/how_can_i_use_the_ivar_uvar_wvar_and_cvar_options_to_precisely_control_the_permutations.md b/faq/clusterstats_iuwcvar.md similarity index 97% rename from faq/how_can_i_use_the_ivar_uvar_wvar_and_cvar_options_to_precisely_control_the_permutations.md rename to faq/clusterstats_iuwcvar.md index c1ff9cf6b..b837a59e9 100644 --- a/faq/how_can_i_use_the_ivar_uvar_wvar_and_cvar_options_to_precisely_control_the_permutations.md +++ b/faq/clusterstats_iuwcvar.md @@ -2,6 +2,8 @@ title: How can I use the ivar, uvar, wvar and cvar options to precisely control the permutations? category: faq tags: [statistics] +redirect_from: + - /faq/how_can_i_use_the_ivar_uvar_wvar_and_cvar_options_to_precisely_control_the_permutations/ --- # How can I use the ivar, uvar, wvar and cvar options to precisely control the permutations? diff --git a/faq/should_I_use_t_or_F_values_for_cluster-based_permutation_tests.md b/faq/clusterstats_teststatistic.md similarity index 97% rename from faq/should_I_use_t_or_F_values_for_cluster-based_permutation_tests.md rename to faq/clusterstats_teststatistic.md index 4b8cdfcbf..2a5fd6c13 100644 --- a/faq/should_I_use_t_or_F_values_for_cluster-based_permutation_tests.md +++ b/faq/clusterstats_teststatistic.md @@ -3,7 +3,9 @@ title: Should I use t or F values for cluster-based permutation tests? category: faq tags: [statistics] authors: [Christoph Huber-Huber] -created: 2023-05-12 +date: 2023-05-12 +redirect_from: + - /faq/should_I_use_t_or_F_values_for_cluster-based_permutation_tests/ --- # Should I use t or F values for cluster-based permutation tests? diff --git a/faq/what_is_the_difference_between_coherence_and_coherency.md b/faq/coherence_coherency.md similarity index 89% rename from faq/what_is_the_difference_between_coherence_and_coherency.md rename to faq/coherence_coherency.md index dd345e942..c0999e1b6 100644 --- a/faq/what_is_the_difference_between_coherence_and_coherency.md +++ b/faq/coherence_coherency.md @@ -2,6 +2,8 @@ title: What is the difference between coherence and coherency? category: faq tags: [coherence] +redirect_from: + - /faq/what_is_the_difference_between_coherence_and_coherency/ --- # What is the difference between coherence and coherency? diff --git a/faq/how_can_i_compile_the_mex_files_on_os_x.md b/faq/compile_osx.md similarity index 94% rename from faq/how_can_i_compile_the_mex_files_on_os_x.md rename to faq/compile_osx.md index 7c71002af..943d476ef 100644 --- a/faq/how_can_i_compile_the_mex_files_on_os_x.md +++ b/faq/compile_osx.md @@ -2,6 +2,8 @@ title: How can I compile the mex files on macOS? category: faq tags: [mex] +redirect_from: + - /faq/how_can_i_compile_the_mex_files_on_os_x/ --- # How can I compile the mex files on macOS? diff --git a/faq/how_can_i_compile_the_mex_files_on_64_bit_windows.md b/faq/compile_windows.md similarity index 96% rename from faq/how_can_i_compile_the_mex_files_on_64_bit_windows.md rename to faq/compile_windows.md index 46ac93839..8950efcf6 100644 --- a/faq/how_can_i_compile_the_mex_files_on_64_bit_windows.md +++ b/faq/compile_windows.md @@ -2,6 +2,8 @@ title: How can I compile the mex files on 64-bit Windows? category: faq tags: [mex, matlab] +redirect_from: + - /faq/how_can_i_compile_the_mex_files_on_64_bit_windows/ --- # How can I compile the mex files on 64-bit Windows? diff --git a/faq/what_is_the_conductivity_of_the_brain_csf_skull_and_skin_tissue.md b/faq/conductivity_defaults.md similarity index 96% rename from faq/what_is_the_conductivity_of_the_brain_csf_skull_and_skin_tissue.md rename to faq/conductivity_defaults.md index 8e07b58f0..58c1c6426 100644 --- a/faq/what_is_the_conductivity_of_the_brain_csf_skull_and_skin_tissue.md +++ b/faq/conductivity_defaults.md @@ -2,6 +2,8 @@ title: What is the conductivity of the brain, CSF, skull and skin tissue? category: faq tags: [headmodel, source] +redirect_from: + - /faq/what_is_the_conductivity_of_the_brain_csf_skull_and_skin_tissue/ --- # What is the conductivity of the brain, CSF, skull and skin tissue? diff --git a/faq/how_can_i_convert_one_dataformat_into_an_other.md b/faq/convert_dataformat.md similarity index 93% rename from faq/how_can_i_convert_one_dataformat_into_an_other.md rename to faq/convert_dataformat.md index ecc029d23..fab90f7fe 100644 --- a/faq/how_can_i_convert_one_dataformat_into_an_other.md +++ b/faq/convert_dataformat.md @@ -2,9 +2,11 @@ title: How can I convert one dataformat into an other? category: faq tags: [dataformat, preprocessing] +redirect_from: + - /faq/how_can_i_convert_one_dataformat_into_an_other/ --- -# How can I convert one dataformat into an other? +# How can I convert one dataformat into another? You can read in the data from the original data format using **[ft_preprocessing](/reference/ft_preprocessing)** and subsequently use the **[ft_write_data](/reference/fileio/ft_write_data)** function to write the data to another format that you can specify. diff --git a/faq/how_can_i_change_the_head_localization_in_a_ctf_dataset.md b/faq/ctf_changeheadloc.md similarity index 97% rename from faq/how_can_i_change_the_head_localization_in_a_ctf_dataset.md rename to faq/ctf_changeheadloc.md index 8c2d23adf..46d629eb2 100644 --- a/faq/how_can_i_change_the_head_localization_in_a_ctf_dataset.md +++ b/faq/ctf_changeheadloc.md @@ -2,6 +2,8 @@ title: How can I change the head localization in a CTF dataset? category: faq tags: [ctf] +redirect_from: + - /faq/how_can_i_change_the_head_localization_in_a_ctf_dataset/ --- # How can I change the head localization in a CTF dataset? diff --git a/faq/i_am_having_problems_reading_the_ctf_.hc_headcoordinates_file.md b/faq/ctf_fixhc.md similarity index 69% rename from faq/i_am_having_problems_reading_the_ctf_.hc_headcoordinates_file.md rename to faq/ctf_fixhc.md index 135379128..913d01cf7 100644 --- a/faq/i_am_having_problems_reading_the_ctf_.hc_headcoordinates_file.md +++ b/faq/ctf_fixhc.md @@ -2,15 +2,17 @@ title: I am having problems reading the CTF .hc headcoordinates file category: faq tags: [ctf, raw] +redirect_from: + - /faq/i_am_having_problems_reading_the_ctf_.hc_headcoordinates_file/ --- # I am having problems reading the CTF .hc headcoordinates file -The most likely problem that you have with your CTF dataset is due to a bug in the dataset itself. Old versions of the CTF acquisition software would write the .hc file with a typo in the file. The file itself is an ASCII file which you can open in any text editor. +The most likely problem that you have with your CTF dataset is due to a bug in the dataset itself. Old versions of the CTF acquisition software would write the .hc file with a typo in the file. The file itself is an ASCII file which you can open (and edit) in any text editor. The 5th line in the file is -'' standard left ear coil position relative to dewar (cm):'' +'' stadard left ear coil position relative to dewar (cm):'' but should be diff --git a/faq/how_can_i_fix_a_corrupt_ctf_meg4_data_file.md b/faq/ctf_fixmeg4.md similarity index 98% rename from faq/how_can_i_fix_a_corrupt_ctf_meg4_data_file.md rename to faq/ctf_fixmeg4.md index 269668bee..ca8a287f8 100644 --- a/faq/how_can_i_fix_a_corrupt_ctf_meg4_data_file.md +++ b/faq/ctf_fixmeg4.md @@ -2,6 +2,8 @@ title: How can I fix a corrupt CTF meg4 file? category: faq tags: [corrupt, ctf, raw] +redirect_from: + - /faq/how_can_i_fix_a_corrupt_ctf_meg4_data_file/ --- # How can I fix a corrupt CTF meg4 file? diff --git a/faq/how_can_i_fix_a_corrupt_ctf_res4_header_file.md b/faq/ctf_fixres4.md similarity index 89% rename from faq/how_can_i_fix_a_corrupt_ctf_res4_header_file.md rename to faq/ctf_fixres4.md index cdf77d4a4..59bcbcd62 100644 --- a/faq/how_can_i_fix_a_corrupt_ctf_res4_header_file.md +++ b/faq/ctf_fixres4.md @@ -2,6 +2,8 @@ title: How can I fix a corrupt CTF res4 header file? category: faq tags: [corrupt, ctf, raw] +redirect_from: + - /faq/how_can_i_fix_a_corrupt_ctf_res4_header_file/ --- # How can I fix a corrupt CTF res4 header file? diff --git a/faq/how_can_i_read_corrupted_unsaved_ctf_data.md b/faq/ctf_readcorrupted.md similarity index 97% rename from faq/how_can_i_read_corrupted_unsaved_ctf_data.md rename to faq/ctf_readcorrupted.md index 497bb3878..745a6d013 100644 --- a/faq/how_can_i_read_corrupted_unsaved_ctf_data.md +++ b/faq/ctf_readcorrupted.md @@ -2,6 +2,8 @@ title: How can I read corrupted (unsaved) CTF data? category: faq tags: [raw, corrupt, preprocessing, ctf] +redirect_from: + - /faq/how_can_i_read_corrupted_unsaved_ctf_data/ --- # How can I read corrupted (unsaved) CTF data? diff --git a/faq/how_does_the_ctf_higher-order_gradiometer_work.md b/faq/ctf_syntheticgradient.md similarity index 94% rename from faq/how_does_the_ctf_higher-order_gradiometer_work.md rename to faq/ctf_syntheticgradient.md index 742b4196a..c0bc8b8a6 100644 --- a/faq/how_does_the_ctf_higher-order_gradiometer_work.md +++ b/faq/ctf_syntheticgradient.md @@ -2,6 +2,8 @@ title: How does the CTF higher-order gradiometer work? category: faq tags: [ctf] +redirect_from: + - /faq/how_does_the_ctf_higher-order_gradiometer_work/ --- # How does the CTF higher-order gradiometer work? @@ -44,7 +46,7 @@ We can explore the different higher order synthetic gradiometer forward solution title(['First order gradiometer forward solution for sensor ' grad.balance.G1BR.labelnew{2}]); xlim([0 175]);ylim([-1.2 1.2]); -{% include image src="/assets/img/faq/how_does_the_ctf_higher-order_gradiometer_work/g1brv.png" %} +{% include image src="/assets/img/faq/ctf_syntheticgradient/g1brv.png" %} The left part of the figure shows how the first order gradiometer forward solution is computed. The X and the Y axes are the MEG sensors inside grad.balance.G1BR.labelnew and grad.balance.G1BR.labelold. The right plot shows how to compute the first order gradiometer for a specific MEG sensor, in this case sensor MLC12, which is the second sensor of the CTF151 system. You can notice that on the x axes the second sensor, the MLC12 scores one, and the rest of the 150 MEG sensors scored zero (blue dots). This is important because the forward computation of the first order gradient is basically constituted by the field contribution of each MEG sensor. However, colored in red, there are some MEG sensors (the environment sensors) that slightly deviated from zero, which means that they're also contribution to the field of sensor MLC12 but with a negligible degree. @@ -61,7 +63,7 @@ If we explore the second and the third synthetic gradiometers, things become ver title(['Second order gradiometer forward solution for sensor ' grad.balance.G2BR.labelnew{2}]); xlim([0 175]);ylim([-1.2 1.2]); -{% include image src="/assets/img/faq/how_does_the_ctf_higher-order_gradiometer_work/g2brv.png" %} +{% include image src="/assets/img/faq/ctf_syntheticgradient/g2brv.png" %} figure; subplot(2,2,[1 3]);imagesc(grad.balance.G3BR.tra); @@ -74,7 +76,7 @@ If we explore the second and the third synthetic gradiometers, things become ver title(['Third order gradiometer forward solution for sensor ' grad.balance.G3BR.labelnew{2}]); xlim([0 175]);ylim([-1.2 1.2]); -{% include image src="/assets/img/faq/how_does_the_ctf_higher-order_gradiometer_work/g3brv.png" %} +{% include image src="/assets/img/faq/ctf_syntheticgradient/g3brv.png" %} Now is more evident that the higher the synthetic gradiometer, the higher the contribution of other MEG sensors to the Nth-order gradiometer forward solution. diff --git a/faq/how_can_i_use_the_databrowser.md b/faq/databrowser.md similarity index 97% rename from faq/how_can_i_use_the_databrowser.md rename to faq/databrowser.md index 713e00693..487168445 100644 --- a/faq/how_can_i_use_the_databrowser.md +++ b/faq/databrowser.md @@ -2,6 +2,8 @@ title: How can I use the databrowser? category: faq tags: [databrowser, plotting, artifact] +redirect_from: + - /faq/how_can_i_use_the_databrowser/ --- # How can I use the databrowser? diff --git a/faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this.md b/faq/databrowser_crash.md similarity index 96% rename from faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this.md rename to faq/databrowser_crash.md index d361b7e3a..7400939d3 100644 --- a/faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this.md +++ b/faq/databrowser_crash.md @@ -2,6 +2,8 @@ title: The databrowser crashes and destroys the whole MATLAB session, how can I resolve this? category: faq tags: [ica, data, crash, databrowser, surf, topoplot, topo] +redirect_from: + - /faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this/ --- # The databrowser crashes and destroys the whole MATLAB session, how can I resolve this? diff --git a/faq/how_can_i_import_my_own_dataformat.md b/faq/dataformat_own.md similarity index 97% rename from faq/how_can_i_import_my_own_dataformat.md rename to faq/dataformat_own.md index 133f9f911..14c35cd19 100644 --- a/faq/how_can_i_import_my_own_dataformat.md +++ b/faq/dataformat_own.md @@ -2,11 +2,13 @@ title: How can I import my own data format? category: faq tags: [dataformat, preprocessing] +redirect_from: + - /faq/how_can_i_import_my_own_dataformat/ --- # How can I import my own data format? -There are two approaches for importing data from an unsupported format: you can extend FieldTrip with new code, or you can circumvent the import procedure. +There are two approaches for importing data from an unsupported format: you can either extend FieldTrip with new code, or you can circumvent the import procedure. ## Extend the FieldTrip reading functions diff --git a/faq/how_should_i_send_example_data_to_the_developers.md b/faq/datasharing.md similarity index 96% rename from faq/how_should_i_send_example_data_to_the_developers.md rename to faq/datasharing.md index 9ef71eccf..090db1dc7 100644 --- a/faq/how_should_i_send_example_data_to_the_developers.md +++ b/faq/datasharing.md @@ -2,6 +2,8 @@ title: How should I share example data with the email list or developers? category: faq tags: [email, development, git] +redirect_from: + - /faq/how_should_i_send_example_data_to_the_developers/ --- # How should I share example data with the email list or developers? diff --git a/faq/how_are_the_various_data_structures_defined.md b/faq/datatype.md similarity index 99% rename from faq/how_are_the_various_data_structures_defined.md rename to faq/datatype.md index a8038f66e..0ef6e9cf1 100644 --- a/faq/how_are_the_various_data_structures_defined.md +++ b/faq/datatype.md @@ -2,6 +2,8 @@ title: How are the various MATLAB data structures defined? category: faq tags: [datatype, dataformat] +redirect_from: + - /faq/how_are_the_various_data_structures_defined/ --- # How are the various MATLAB data structures defined? diff --git a/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip.md b/faq/datatype_freq.md similarity index 98% rename from faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip.md rename to faq/datatype_freq.md index 1e11584b4..bc30679a2 100644 --- a/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip.md +++ b/faq/datatype_freq.md @@ -2,6 +2,8 @@ title: In what way can frequency domain data be represented in FieldTrip? category: faq tags: [freq, connectivity, coherence] +redirect_from: + - /faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip/ --- # In what way can frequency domain data be represented in FieldTrip? diff --git a/faq/what_kind_of_volume_conduction_models_are_implemented.md b/faq/datatype_headmodel.md similarity index 96% rename from faq/what_kind_of_volume_conduction_models_are_implemented.md rename to faq/datatype_headmodel.md index f82a52b3b..b74e8c6e8 100644 --- a/faq/what_kind_of_volume_conduction_models_are_implemented.md +++ b/faq/datatype_headmodel.md @@ -2,6 +2,8 @@ title: What kind of volume conduction models of the head (head models) are implemented? category: faq tags: [headmodel, source] +redirect_from: + - /faq/what_kind_of_volume_conduction_models_are_implemented/ --- # What kind of volume conduction models of the head (head models) are implemented? diff --git a/faq/how_is_the_segmentation_defined.md b/faq/datatype_segmentation.md similarity index 91% rename from faq/how_is_the_segmentation_defined.md rename to faq/datatype_segmentation.md index 076e2d0d6..c35375615 100644 --- a/faq/how_is_the_segmentation_defined.md +++ b/faq/datatype_segmentation.md @@ -2,6 +2,8 @@ title: How is the segmentation defined? category: faq tags: [datatype, segmentation, eeg, meg, headmodel] +redirect_from: + - /faq/how_is_the_segmentation_defined/ --- # How is the segmentation defined? @@ -26,9 +28,9 @@ The tissue type of each voxel can be represented in the FieldTrip structure in t The default output of the ft_volumesegment function (see above) is a segmentation data-type structure with probabilistic tissue maps. The **gray**, **white** and **csf** fields contain _probabilistic values_ for representing the gray, white matter and the cerebrospinal fluid. This means, for example, that at the field **white** everything that is not the white matter represented by 0, and voxels which belong to the white matter have a value between 0 and 1. -{% include image src="/assets/img/faq/how_is_the_segmentation_defined/gray.png" width="186" %} -{% include image src="/assets/img/faq/how_is_the_segmentation_defined/white.png" width="186" %} -{% include image src="/assets/img/faq/how_is_the_segmentation_defined/csf.png" width="186" %} +{% include image src="/assets/img/faq/datatype_segmentation/gray.png" width="186" %} +{% include image src="/assets/img/faq/datatype_segmentation/white.png" width="186" %} +{% include image src="/assets/img/faq/datatype_segmentation/csf.png" width="186" %} _Figure 1. Probabilistic maps of the gray (left), white (middle) and cerebrospinal fluid (right). The colors represent probabilities ranging from 0 to 1._ @@ -63,9 +65,9 @@ The reason for this is explained in more detail [here](/faq/how_change_mri_orien When the brain, skull and scalp tissues are requested as outputs from ft_volumesegment, the output also represents the probabilistic representation. However, in this case each fields contain a binary or boolean value, i.e. a probability of 0 (false) or 1 (true). Hence, the binary representation is a special case of the probabilistic representation. -{% include image src="/assets/img/faq/how_is_the_segmentation_defined/brain.png" width="186" %} -{% include image src="/assets/img/faq/how_is_the_segmentation_defined/skull.png" width="186" %} -{% include image src="/assets/img/faq/how_is_the_segmentation_defined/scalp.png" width="186" %} +{% include image src="/assets/img/faq/datatype_segmentation/brain.png" width="186" %} +{% include image src="/assets/img/faq/datatype_segmentation/skull.png" width="186" %} +{% include image src="/assets/img/faq/datatype_segmentation/scalp.png" width="186" %} _Figure 2. The brain (left), the skull (middle) and scalp (right). The colors represent only zeros and ones._ @@ -105,7 +107,7 @@ Regardless of whether the probabilities are crisp (i.e. either exactly 0 or 1) o When only the scalp as output is required from the segmentation, the scalp-mask includes also the brain and skull tissues. -{% include image src="/assets/img/faq/how_is_the_segmentation_defined/scalponly.png" width="200" %} +{% include image src="/assets/img/faq/datatype_segmentation/scalponly.png" width="200" %} _Figure 3. The binary representation of the outside surface of the scalp. The colors represent only zeros and ones._ @@ -144,7 +146,7 @@ In this structure, the **brick0** and **brick1** field contains two different in An indexed representation can also be plotted to inspect the different tissues in an image (see below). -{% include image src="/assets/img/faq/how_is_the_segmentation_defined/afni_atlas.png" width="300" %} +{% include image src="/assets/img/faq/datatype_segmentation/afni_atlas.png" width="300" %} _Figure 4. Plot of the integer values that are represented in the indexed "brick0" representation of the AFNI atlas. The figure was made with "colormap lines"._ @@ -169,7 +171,7 @@ The following code demonstrates how to create an indexed representation from the colormap(map); -{% include image src="/assets/img/faq/how_is_the_segmentation_defined/seg_indexed.png" width="350" %} +{% include image src="/assets/img/faq/datatype_segmentation/seg_indexed.png" width="350" %} _Figure 5. The brain (blue), skull (green) and scalp (red) after segmentation with indexing. The colors represent integers from zero to three._ @@ -179,6 +181,6 @@ An indexed segmentation can represent only non-overlapping tissues/brain areas, When a non-binary probabilistic segmentation is used and when the binary representations of the different tissue types partially overlap, the conversion to an indexed representation would involve a disambiguation of each voxel to which tissue/brain area it belongs to and the more fine-grade information of the probability values would disappear. -{% include image src="/assets/img/faq/how_is_the_segmentation_defined/tissue_representation.png" width="500" %} +{% include image src="/assets/img/faq/datatype_segmentation/tissue_representation.png" width="500" %} _Figure 6. Schematic figure of conversion between different representation of the segmentation. Binary probabilistic representation of non-overlapping tissue-types can be directly converted to an indexed representation (A). When an overlapping or/and non-binary probabilistic representation is converted to indexed, the representations are not equivalent (B)_ diff --git a/faq/how_is_anatomical_functional_or_statistical_volume_data_described.md b/faq/datatype_volume.md similarity index 97% rename from faq/how_is_anatomical_functional_or_statistical_volume_data_described.md rename to faq/datatype_volume.md index 572984587..a6683e01f 100644 --- a/faq/how_is_anatomical_functional_or_statistical_volume_data_described.md +++ b/faq/datatype_volume.md @@ -2,6 +2,8 @@ title: How is anatomical, functional or statistical "volume data" described? category: faq tags: [volume, datatype] +redirect_from: + - /faq/how_is_anatomical_functional_or_statistical_volume_data_described/ --- # How is anatomical, functional or statistical "volume data" described? diff --git a/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter.md b/faq/dftfilter_residual.md similarity index 85% rename from faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter.md rename to faq/dftfilter_residual.md index 17d35b59f..eff98e437 100644 --- a/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter.md +++ b/faq/dftfilter_residual.md @@ -2,13 +2,15 @@ title: Why is there a residual 50Hz line-noise component after applying a DFT filter? category: faq tags: [artifact, filter, noise, preprocessing] +redirect_from: + - /faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter/ --- # Why is there a residual 50Hz line-noise component after applying a DFT filter? The residual line noise at 50 or 60 Hz is due to its non-stationarity. Imagine a trial in which the 50Hz line noise increases in amplitude over time (e.g., trial #3 in the first figure). -{% include image src="/assets/img/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter/linenoise.png" width="600" %} +{% include image src="/assets/img/faq/dftfilter_residual/linenoise.png" width="600" %} With `cfg.dftfilter` we fit the amplitude and phase of a constant-amplitude sine wave to the data. The fitted amplitude will correspond to the mean over the whole trial, i.e. at the begin of the trial it will be larger than the actual amplitude, and towards the end it will be smaller (second figure, using a 5 Hz example sine). @@ -30,7 +32,7 @@ With `cfg.dftfilter` we fit the amplitude and phase of a constant-amplitude sine s2 = avgamp.*sin(2*pi*f*t); hold on; plot(t, s2, 'r'); -{% include image src="/assets/img/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter/dftfilter1.png" width="500" %} +{% include image src="/assets/img/faq/dftfilter_residual/dftfilter1.png" width="500" %} Imagine that you then subtracting the estimated 5 Hz component. At the begin of the trial you subtract too much, causing a negative (sign-flipped) 5 Hz signal to remain in the data, and towards the end of the trial you are not subtracting enough, causing a positive (non sign-flipped) 5 Hz signal to remain (black line in third figure). @@ -44,7 +46,7 @@ So computed over the whole time interval of the cleaned data, the 5 Hz amplitude s4 = ft_preproc_bandstopfilter(s1, fs, [4.9 5.1], 2); hold on; plot(t, s4, 'm'); -{% include image src="/assets/img/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter/dftfilter2.png" width="500" %} +{% include image src="/assets/img/faq/dftfilter_residual/dftfilter2.png" width="500" %} After spectral estimation this would lead to a consistent decrease in the line noise towards the middle of the trials. Note that it depends on the spectral estimation technique and the data padding during filtering whether and how the residual line noise will express itself. diff --git a/faq/where_can_i_find_the_dipoli_command-line_executable.md b/faq/dipoli_filelocation.md similarity index 83% rename from faq/where_can_i_find_the_dipoli_command-line_executable.md rename to faq/dipoli_filelocation.md index 0409f132b..258b0a88f 100644 --- a/faq/where_can_i_find_the_dipoli_command-line_executable.md +++ b/faq/dipoli_filelocation.md @@ -2,14 +2,17 @@ title: Where can I find the dipoli command-line executable? category: faq tags: [headmodel, source, matlab] +redirect_from: + - /faq/where_can_i_find_the_dipoli_command-line_executable/ --- # Where can I find the dipoli command-line executable? The Boundary Element Method (BEM) allows for source reconstruction of EEG data with realistic head geometries. FieldTrip implements the BEM method for EEG in a general fashion in the forward **[ft_compute_leadfield](/reference/forward/ft_compute_leadfield)** function. However, this requires that a previously prepared BEM model is passed to the **[ft_sourceanalysis](/reference/ft_sourceanalysis)** function or to the **[ft_dipolefitting](/reference/ft_dipolefitting)** function. To construct such an EEG BEM model, you can use the **[ft_prepare_headmodel](/reference/ft_prepare_headmodel)** function, where in cfg.method you should specify `dipoli`, `bemcp` or `openmeeg`. -Dipoli is a command line application that was developed by [Thom Oostendorp](http://www.mbfys.ru.nl/~thom). A compiled version for Linux, macOS and Windows is included in `fieldtrip/external/dipoli`. Note that the Windows version cannot be called directly from within MATLAB. +Dipoli is a command line application that was developed by [Thom Oostendorp](http://www.mbfys.ru.nl/~thom). A compiled version for Linux, macOS and Windows is included in `fieldtrip/external/dipoli`. As of september 2024, it is also possible to call the Windows executable directly from the FieldTrip code (previously it was not). ## Linux +(NOTE: the below is probably outdated, and needs checking) The dipoli executable for Linux was compiled on a 32-bit system. To run it on a 64-bit system, you need to install the "ia32-libs" library (sudo apt-get install ia32-libs). On newer systems, ia32-libs are deprecated so you should enable the i386 architecture (sudo dpkg --add-architecture i386 && sudo apt-get update) and install the 32-bit libraries (sudo apt-get install libc6:i386 libstdc++6:i386). diff --git a/faq/how_can_i_distribute_a_batch_of_jobs.md b/faq/distributed_batch.md similarity index 98% rename from faq/how_can_i_distribute_a_batch_of_jobs.md rename to faq/distributed_batch.md index 02fc865bf..cc8156c4c 100644 --- a/faq/how_can_i_distribute_a_batch_of_jobs.md +++ b/faq/distributed_batch.md @@ -2,6 +2,8 @@ title: How can I distribute a batch of jobs? category: faq tags: [distcomp] +redirect_from: + - /faq/how_can_i_distribute_a_batch_of_jobs/ --- # How can I distribute a batch of jobs? diff --git a/faq/what_are_the_different_approaches_i_can_take_for_distributed_computing.md b/faq/distributed_computing.md similarity index 98% rename from faq/what_are_the_different_approaches_i_can_take_for_distributed_computing.md rename to faq/distributed_computing.md index e15378aa8..f6fc7036d 100644 --- a/faq/what_are_the_different_approaches_i_can_take_for_distributed_computing.md +++ b/faq/distributed_computing.md @@ -2,6 +2,8 @@ title: What are the different approaches I can take for distributed computing? category: faq tags: [qsub, parfor, distcomp, matlab] +redirect_from: + - /faq/what_are_the_different_approaches_i_can_take_for_distributed_computing/ --- # What are the different approaches I can take for distributed computing? diff --git a/faq/how_to_get_started_with_the_matlab_distributed_computing_toolbox.md b/faq/distributed_matlab.md similarity index 97% rename from faq/how_to_get_started_with_the_matlab_distributed_computing_toolbox.md rename to faq/distributed_matlab.md index 62b9da3e5..4f32d6335 100644 --- a/faq/how_to_get_started_with_the_matlab_distributed_computing_toolbox.md +++ b/faq/distributed_matlab.md @@ -2,6 +2,8 @@ title: How to get started with the MATLAB distributed computing toolbox? category: faq tags: [distcomp, parfor] +redirect_from: + - /faq/how_to_get_started_with_the_matlab_distributed_computing_toolbox/ --- # How to get started with the MATLAB distributed computing toolbox? diff --git a/faq/how_to_get_started_with_distributed_computing_using_qsub.md b/faq/distributed_qsub.md similarity index 99% rename from faq/how_to_get_started_with_distributed_computing_using_qsub.md rename to faq/distributed_qsub.md index 82488edb2..945e080a1 100644 --- a/faq/how_to_get_started_with_distributed_computing_using_qsub.md +++ b/faq/distributed_qsub.md @@ -2,6 +2,8 @@ title: How to get started with distributed computing using qsub? category: faq tags: [qsub] +redirect_from: + - /faq/how_to_get_started_with_distributed_computing_using_qsub/ --- # How to get started with distributed computing using qsub? diff --git a/faq/can_i_get_an_offline_version_of_the_wiki_documentation.md b/faq/documentation_offline.md similarity index 83% rename from faq/can_i_get_an_offline_version_of_the_wiki_documentation.md rename to faq/documentation_offline.md index 8514d6e7b..1dd05e1c9 100644 --- a/faq/can_i_get_an_offline_version_of_the_wiki_documentation.md +++ b/faq/documentation_offline.md @@ -2,6 +2,8 @@ title: Can I get an offline version of the documentation on the website? category: faq tags: [documentation] +redirect_from: + - /faq/can_i_get_an_offline_version_of_the_documentation/ --- # Can I get an offline version of the documentation on the website? diff --git a/faq/i_am_working_at_the_donders_should_i_also_download_fieldtrip.md b/faq/download_donders.md similarity index 92% rename from faq/i_am_working_at_the_donders_should_i_also_download_fieldtrip.md rename to faq/download_donders.md index d4597aa07..e0e083b56 100644 --- a/faq/i_am_working_at_the_donders_should_i_also_download_fieldtrip.md +++ b/faq/download_donders.md @@ -2,6 +2,8 @@ title: I am working at the Donders, should I also download FieldTrip? category: faq tags: [path, download] +redirect_from: + - /faq/i_am_working_at_the_donders_should_i_also_download_fieldtrip/ --- # I am working at the Donders, should I also download FieldTrip? diff --git a/faq/i_am_having_problems_downloading.md b/faq/download_ftpproblem.md similarity index 97% rename from faq/i_am_having_problems_downloading.md rename to faq/download_ftpproblem.md index 1fa80f615..906e724e6 100644 --- a/faq/i_am_having_problems_downloading.md +++ b/faq/download_ftpproblem.md @@ -4,6 +4,7 @@ category: faq tags: [download, release] redirect_from: - /faq/i_am_having_problems_downloading_from_the_ftp_server/ + - /faq/i_am_having_problems_downloading/ --- # I am having problems downloading diff --git a/faq/how_can_i_download_a_specific_version.md b/faq/download_version.md similarity index 95% rename from faq/how_can_i_download_a_specific_version.md rename to faq/download_version.md index 7ab593411..61413ef27 100644 --- a/faq/how_can_i_download_a_specific_version.md +++ b/faq/download_version.md @@ -2,6 +2,8 @@ title: Which version of FieldTrip should I download? category: faq tags: [download, release] +redirect_from: + - /faq/how_can_i_download_a_specific_version/ --- Our [download server](https://download.fieldtriptoolbox.org/) holds recent versions of the FieldTrip toolbox code, corresponding to [tagged versions](https://github.com/fieldtrip/fieldtrip/tags) on GitHub. In general we also archive the latest released version of every year on , which correspond to the persistently archived versions on [Zenodo](https://zenodo.org/records/10495308). diff --git a/faq/how_can_i_read_all_channels_from_an_edf_file_that_contains_multiple_sampling_rates.md b/faq/edf2fieldtrip.md similarity index 91% rename from faq/how_can_i_read_all_channels_from_an_edf_file_that_contains_multiple_sampling_rates.md rename to faq/edf2fieldtrip.md index 79e6a8070..01fa767db 100644 --- a/faq/how_can_i_read_all_channels_from_an_edf_file_that_contains_multiple_sampling_rates.md +++ b/faq/edf2fieldtrip.md @@ -2,6 +2,8 @@ title: How can I read all channels from an EDF file that contains multiple sampling rates? category: faq tags: [edf, preprocessing] +redirect_from: + - /faq/how_can_i_read_all_channels_from_an_edf_file_that_contains_multiple_sampling_rates/ --- # How can I read all channels from an EDF file that contains multiple sampling rates? diff --git a/faq/how_can_i_determine_the_onset_of_an_effect.md b/faq/effectonset.md similarity index 97% rename from faq/how_can_i_determine_the_onset_of_an_effect.md rename to faq/effectonset.md index 3808cd170..c362f9ba3 100644 --- a/faq/how_can_i_determine_the_onset_of_an_effect.md +++ b/faq/effectonset.md @@ -2,6 +2,8 @@ title: How can I determine the onset of an effect? category: faq tags: [statistics] +redirect_from: + - /faq/how_can_i_determine_the_onset_of_an_effect/ --- # How can I determine the onset of an effect? diff --git a/faq/how_can_i_read_egi_mff_data_without_the_jvm.md b/faq/egi_nojvm.md similarity index 94% rename from faq/how_can_i_read_egi_mff_data_without_the_jvm.md rename to faq/egi_nojvm.md index fc374bec8..f4330851a 100644 --- a/faq/how_can_i_read_egi_mff_data_without_the_jvm.md +++ b/faq/egi_nojvm.md @@ -2,6 +2,8 @@ title: How can I read EGI mff data without the JVM? category: faq tags: [egi] +redirect_from: + - /faq/how_can_i_read_egi_mff_data_without_the_jvm/ --- # How can I read EGI mff data without the JVM? diff --git a/faq/why_am_i_receiving_warnings_about_too_many_bouncing_emails.md b/faq/emaillist_bounces.md similarity index 95% rename from faq/why_am_i_receiving_warnings_about_too_many_bouncing_emails.md rename to faq/emaillist_bounces.md index 40a886e9d..7dedcaf80 100644 --- a/faq/why_am_i_receiving_warnings_about_too_many_bouncing_emails.md +++ b/faq/emaillist_bounces.md @@ -2,6 +2,8 @@ title: Why am I receiving warnings about too many bouncing emails? category: faq tags: [email] +redirect_from: + - /faq/why_am_i_receiving_warnings_about_too_many_bouncing_emails/ --- # Why am I receiving warnings about too many bouncing emails? diff --git a/faq/how_to_ask_good_questions_to_the_community.md b/faq/emaillist_howtoask.md similarity index 97% rename from faq/how_to_ask_good_questions_to_the_community.md rename to faq/emaillist_howtoask.md index ac74a3664..2ad5985ce 100644 --- a/faq/how_to_ask_good_questions_to_the_community.md +++ b/faq/emaillist_howtoask.md @@ -2,13 +2,15 @@ title: How to ask good questions to the community? category: faq tags: [support, email] +redirect_from: + - /faq/how_to_ask_good_questions_to_the_community/ --- # How to ask good questions to the community? The FieldTrip community is represented on the [email discussion list](/discussion_list). You can also sign up and ask for help if you are stuck in using FieldTrip. Asking good questions there (and giving useful answers) is the key to a successful community. However, please do some research yourself on them before approaching fellow researchers on the discussion list. Keep in mind that several hundreds of researchers around the world will get note of your question and will spend their valuable time on reading your question. In addition, also keep career perspectives into mind. By asking your first question on the mailing list (which could be before you wrote your first paper), they will get a first impression of you and may start to form a picture of you, be it as a prospective colleague or collaborator. Many of the members are senior researchers and might have a job opening and are looking for you! But, don't be afraid to ask questions, we really appreciate if you approach us and we will try to help, even if your question turns out to have a trivial answer :) -{% include image src="/assets/img/faq/how_to_ask_good_questions_to_the_community/peanutsediting.jpg" width="400" %} +{% include image src="/assets/img/faq/emaillist_howtoask/peanutsediting.jpg" width="400" %} To facilitate you in asking good quality questions, this FAQ serves as a guide for diff --git a/faq/why_am_i_not_allowed_to_post_to_the_discussion_list.md b/faq/emaillist_nopost.md similarity index 95% rename from faq/why_am_i_not_allowed_to_post_to_the_discussion_list.md rename to faq/emaillist_nopost.md index 373edbfe9..555f82451 100644 --- a/faq/why_am_i_not_allowed_to_post_to_the_discussion_list.md +++ b/faq/emaillist_nopost.md @@ -2,6 +2,8 @@ title: Why am I not allowed to post to the discussion list? category: faq tags: [email] +redirect_from: + - /faq/why_am_i_not_allowed_to_post_to_the_discussion_list/ --- # Why am I not allowed to post to the discussion list? diff --git a/faq/why_am_i_not_receiving_emails_from_the_discussion_list.md b/faq/emaillist_noreceive.md similarity index 90% rename from faq/why_am_i_not_receiving_emails_from_the_discussion_list.md rename to faq/emaillist_noreceive.md index 5c5052e87..427389dc0 100644 --- a/faq/why_am_i_not_receiving_emails_from_the_discussion_list.md +++ b/faq/emaillist_noreceive.md @@ -2,6 +2,8 @@ title: Why am I not receiving emails from the discussion list? category: faq tags: [email] +redirect_from: + - /faq/why_am_i_not_receiving_emails_from_the_discussion_list/ --- # Why am I not receiving emails from the discussion list? diff --git a/faq/why_is_my_message_rejected_from_the_email_discussion_list.md b/faq/emaillist_rejected.md similarity index 94% rename from faq/why_is_my_message_rejected_from_the_email_discussion_list.md rename to faq/emaillist_rejected.md index 8cd43b729..d0a245fbb 100644 --- a/faq/why_is_my_message_rejected_from_the_email_discussion_list.md +++ b/faq/emaillist_rejected.md @@ -2,6 +2,8 @@ title: Why is my message rejected from the email discussion list? category: faq tags: [email] +redirect_from: + - /faq/why_is_my_message_rejected_from_the_email_discussion_list/ --- # Why is my message rejected from the email discussion list? diff --git a/faq/how_many_people_are_subscribed_to_the_email_discussion_list.md b/faq/emaillist_subscribers.md similarity index 74% rename from faq/how_many_people_are_subscribed_to_the_email_discussion_list.md rename to faq/emaillist_subscribers.md index 912fd7b3e..aa3a7be50 100644 --- a/faq/how_many_people_are_subscribed_to_the_email_discussion_list.md +++ b/faq/emaillist_subscribers.md @@ -2,6 +2,8 @@ title: How many people are subscribed to the email discussion list? category: faq tags: [email] +redirect_from: + - /faq/how_many_people_are_subscribed_to_the_email_discussion_list/ --- # How many people are subscribed to the email discussion list? diff --git a/faq/what_is_the_relation_between_events_such_as_triggers_and_trials.md b/faq/eventsversustrials.md similarity index 97% rename from faq/what_is_the_relation_between_events_such_as_triggers_and_trials.md rename to faq/eventsversustrials.md index cd3b9a5da..dacc987f0 100644 --- a/faq/what_is_the_relation_between_events_such_as_triggers_and_trials.md +++ b/faq/eventsversustrials.md @@ -2,6 +2,8 @@ title: What is the relation between "events" (such as triggers) and "trials"? category: faq tags: [preprocessing, trialfun] +redirect_from: + - /faq/what_is_the_relation_between_events_such_as_triggers_and_trials/ --- # What is the relation between "events" (such as triggers) and "trials"? @@ -40,7 +42,7 @@ After translating the event table into an Nx3 trial definition (cfg.trl), the da For a better understanding of the relation between the event offset, trials (or data segments) and the time axis of trials, it helps to look at a number of samples in detail. In the picture below a sampling rate of 1000 Hz is used to allow a simple translation between samples and miliseconds. Remember that FieldTrip works with seconds and not with miliseconds. -{% include image src="/assets/img/faq/what_is_the_relation_between_events_such_as_triggers_and_trials/offset.png" width="600" %} +{% include image src="/assets/img/faq/eventsversustrials/offset.png" width="600" %} The first row (A) in the figure above shows the samples and the sample numbers. The first sample of the recording (i.e. of the file as stored on disk) is sample 1. Here it is assumed that the sampling rate is 1000 Hz, i.e. one sample per milisecond. diff --git a/faq/fiducial.md b/faq/fiducial.md index c46aabc41..45d52fd9b 100644 --- a/faq/fiducial.md +++ b/faq/fiducial.md @@ -26,4 +26,4 @@ In **[ft_electroderealign](/reference/ft_electroderealign)** the fiducials are n In case fiducials are present in the `elec` structure, they will simply be removed at the time of forward modeling. Just like channels such as “trigger” and “EOG” are removed from the data prior to forward modeling. -See also the related documentation that explains [how electrodes, magnetometers or gradiometers are described](/faq/how_are_electrodes_magnetometers_or_gradiometers_described) and that explains [how to report the positions of the fiducial points on the head](/faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head). +See also the related documentation that explains [how electrodes, magnetometers or gradiometers are described](/faq/sensors_definition) and that explains [how to report the positions of the fiducial points on the head](/faq/fiducials_definition). diff --git a/faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head.md b/faq/fiducials_definition.md similarity index 94% rename from faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head.md rename to faq/fiducials_definition.md index 2e9ace678..e2fd5b5c3 100644 --- a/faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head.md +++ b/faq/fiducials_definition.md @@ -2,6 +2,8 @@ title: How should I report the positions of the fiducial points on the head? category: faq tags: [electrode, fiducial, polhemus, coordinate] +redirect_from: + - /faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head/ --- # How should I report the positions of the fiducial points on the head? @@ -25,7 +27,7 @@ Clarity and precision in the definition and measurement of the fiducial points c - LHS/RHS - Left and Right Helix-Scalp junction - blue dot - LHJ/RHJ - Left and Right Helix-Tragus Junction - red dot -{% include image src="/assets/img/faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head/fiducial_points.png" width="350" %} +{% include image src="/assets/img/faq/fiducials_definition/fiducial_points.png" width="350" %} {% include markup/skyblue %} The Helix-Tragus Junction (i.e. LHJ and RHJ) is the best defined in anatomical MRIs and in 3D scans. diff --git a/faq/how_many_lines_of_code_does_fieldtrip_consist_of.md b/faq/fieldtrip_codelines.md similarity index 94% rename from faq/how_many_lines_of_code_does_fieldtrip_consist_of.md rename to faq/fieldtrip_codelines.md index 8df74a06f..cbffd8f16 100644 --- a/faq/how_many_lines_of_code_does_fieldtrip_consist_of.md +++ b/faq/fieldtrip_codelines.md @@ -2,6 +2,8 @@ title: How many lines of code does FieldTrip consist of? category: faq tags: [matlab] +redirect_from: + - /faq/how_many_lines_of_code_does_fieldtrip_consist_of/ --- # How many lines of code does FieldTrip consist of? diff --git a/faq/which_version_of_fieldtrip_should_i_download.md b/faq/fieldtrip_downloadversion.md similarity index 97% rename from faq/which_version_of_fieldtrip_should_i_download.md rename to faq/fieldtrip_downloadversion.md index 4d16c8f28..98f6550f9 100644 --- a/faq/which_version_of_fieldtrip_should_i_download.md +++ b/faq/fieldtrip_downloadversion.md @@ -4,6 +4,7 @@ category: faq tags: [download, release] redirect_from: - /faq/which_version_of_fieldtrip_should_i_download_from_the_ftp_server/ + - /faq/which_version_of_fieldtrip_should_i_download/ --- # Which version of FieldTrip should I download? diff --git a/faq/why_is_fieldtrip_developed_separately_from_eeglab.md b/faq/fieldtrip_eeglab.md similarity index 97% rename from faq/why_is_fieldtrip_developed_separately_from_eeglab.md rename to faq/fieldtrip_eeglab.md index 8e4e8fb4c..c591f87d9 100644 --- a/faq/why_is_fieldtrip_developed_separately_from_eeglab.md +++ b/faq/fieldtrip_eeglab.md @@ -2,6 +2,8 @@ title: Why is FieldTrip developed separately from EEGLAB? category: faq tags: [eeglab] +redirect_from: + - /faq/why_is_fieldtrip_developed_separately_from_eeglab/ --- # Why is FieldTrip developed separately from EEGLAB? diff --git a/faq/what_does_a_typical_call_to_a_fieldtrip_function_look_like.md b/faq/fieldtrip_functioncall.md similarity index 91% rename from faq/what_does_a_typical_call_to_a_fieldtrip_function_look_like.md rename to faq/fieldtrip_functioncall.md index 575f42d84..3f50410c3 100644 --- a/faq/what_does_a_typical_call_to_a_fieldtrip_function_look_like.md +++ b/faq/fieldtrip_functioncall.md @@ -2,6 +2,8 @@ title: What does a typical call to a FieldTrip function look like? category: faq tags: [datatype, function] +redirect_from: + - /faq/what_does_a_typical_call_to_a_fieldtrip_function_look_like/ --- # What does a typical call to a FieldTrip function look like? diff --git a/faq/how_should_i_refer_to_fieldtrip_in_my_publication.md b/faq/fieldtrip_reference.md similarity index 94% rename from faq/how_should_i_refer_to_fieldtrip_in_my_publication.md rename to faq/fieldtrip_reference.md index 44e0a6879..52646c1ad 100644 --- a/faq/how_should_i_refer_to_fieldtrip_in_my_publication.md +++ b/faq/fieldtrip_reference.md @@ -2,6 +2,8 @@ title: How should I refer to FieldTrip in my publication? category: faq tags: [reference] +redirect_from: + - /faq/how_should_i_refer_to_fieldtrip_in_my_publication/ --- # How should I refer to FieldTrip in my publication? diff --git a/faq/does_the_fieldtrip_realtime_buffer_only_work_with_matlab.md b/faq/fieldtripbuffer.md similarity index 96% rename from faq/does_the_fieldtrip_realtime_buffer_only_work_with_matlab.md rename to faq/fieldtripbuffer.md index 01b94ae47..fea4e127e 100644 --- a/faq/does_the_fieldtrip_realtime_buffer_only_work_with_matlab.md +++ b/faq/fieldtripbuffer.md @@ -2,6 +2,8 @@ title: Does the FieldTrip realtime buffer only work with MATLAB? category: faq tags: [realtime] +redirect_from: + - /faq/does_the_fieldtrip_realtime_buffer_only_work_with_matlab/ --- # Does the FieldTrip realtime buffer only work with MATLAB? diff --git a/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer.md b/faq/fieldtripbuffer_gettingstarted.md similarity index 84% rename from faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer.md rename to faq/fieldtripbuffer_gettingstarted.md index 923b4e7a9..4fb3fd54c 100644 --- a/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer.md +++ b/faq/fieldtripbuffer_gettingstarted.md @@ -2,6 +2,8 @@ title: How should I get started with the FieldTrip realtime buffer? category: faq tags: [realtime] +redirect_from: + - /faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/ --- # How should I get started with the FieldTrip realtime buffer? @@ -30,13 +32,13 @@ The buffer application does not show anything, it only starts the buffer, which The sine2ft and viewer initially looks like this: -{% include image src="/assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/sine2ft.png" width="300" %} -{% include image src="/assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/bufferviewer.png" width="400" %} +{% include image src="/assets/img/faq/fieldtripbuffer_gettingstarted/sine2ft.png" width="300" %} +{% include image src="/assets/img/faq/fieldtripbuffer_gettingstarted/bufferviewer.png" width="400" %} If you click "start" in the sine2ft window, and subsequently "connect" in the viewer window, you will see that data starts streaming from sine2ft->buffer->viewer. -{% include image src="/assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/sine2ft_running.png" width="300" %} -{% include image src="/assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/bufferviewer_running.png" width="400" %} +{% include image src="/assets/img/faq/fieldtripbuffer_gettingstarted/sine2ft_running.png" width="300" %} +{% include image src="/assets/img/faq/fieldtripbuffer_gettingstarted/bufferviewer_running.png" width="400" %} ## Connect from MATLAB @@ -72,7 +74,7 @@ Subsequently you could do to see the amount of data in the buffer steadily increasing over time. Note that all channels have exactly the same value, hence you will only see a single sine wave. -{% include image src="/assets/img/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer/screen_shot_2013-11-12_at_17.05.01.png" width="400" %} +{% include image src="/assets/img/faq/fieldtripbuffer_gettingstarted/screen_shot_2013-11-12_at_17.05.01.png" width="400" %} After a certain amount of time, the [ring buffer](https://en.wikipedia.org/wiki/Circular_buffer) will fill up and start wrapping around. From that point onward you will not be able to read the data all the way back from sample 1. diff --git a/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming.md b/faq/fieldtripbuffer_speed.md similarity index 95% rename from faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming.md rename to faq/fieldtripbuffer_speed.md index 5eafe25c8..94b9a12b4 100644 --- a/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming.md +++ b/faq/fieldtripbuffer_speed.md @@ -2,6 +2,8 @@ title: How fast is the FieldTrip buffer for realtime data streaming? category: faq tags: [realtime, matlab, memory] +redirect_from: + - /faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming/ --- # How fast is the FieldTrip buffer for realtime data streaming? @@ -16,14 +18,14 @@ The following benchmarks have been run using the **rt_benchmark** script in the The first name in the legend always refers to the machine where the **rt_benchmark** script was run from, whereas the other name behind the dash refers to the machine that contained the buffer, with the exception of **dma**, which means that the buffer was kept in the same MATLAB instance, thus involving no TCP/IP communication. -{% include image src="/assets/img/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming/benchmark_w.png" %} -{% include image src="/assets/img/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming/benchmark_r.png" %} +{% include image src="/assets/img/faq/fieldtripbuffer_speed/benchmark_w.png" %} +{% include image src="/assets/img/faq/fieldtripbuffer_speed/benchmark_r.png" %} The dramatic dip for the mentat2xx-localhost connections needs further investigation. Update 19-08-2010: After implementing an alternative communication channel using local UNIX domain sockets, here is an updated figure for a single 64-bit Linux machine. Communication over local domain sockets is generally faster, but most importantly, it is more consistent across blocksizes and scales linearly like the DMA throughput. -{% include image src="/assets/img/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming/mentat201_tcp_vs_unix.png" %} +{% include image src="/assets/img/faq/fieldtripbuffer_speed/mentat201_tcp_vs_unix.png" %} ## Older comparisons involving Apple computers diff --git a/faq/can_i_use_the_fieldtrip_logo_on_my_poster.md b/faq/fieldtriplogo.md similarity index 93% rename from faq/can_i_use_the_fieldtrip_logo_on_my_poster.md rename to faq/fieldtriplogo.md index 09e370d73..4dba33c02 100644 --- a/faq/can_i_use_the_fieldtrip_logo_on_my_poster.md +++ b/faq/fieldtriplogo.md @@ -2,6 +2,9 @@ title: Can I use the FieldTrip logo on my poster? category: faq tags: [logo] +redirect_from: + - /faq/can_i_use_the_fieldtrip_logo_on_my_poster/ + --- # Can I use the FieldTrip logo on my poster or elsewhere? diff --git a/faq/what_is_a_good_way_to_save_images_for_later_processing_in_other_software.md b/faq/figure_export.md similarity index 95% rename from faq/what_is_a_good_way_to_save_images_for_later_processing_in_other_software.md rename to faq/figure_export.md index 1b22373b1..b0565c600 100644 --- a/faq/what_is_a_good_way_to_save_images_for_later_processing_in_other_software.md +++ b/faq/figure_export.md @@ -2,6 +2,8 @@ title: What is a good way to save images for later processing in other software? category: faq tags: [plotting] +redirect_from: + - /faq/what_is_a_good_way_to_save_images_for_later_processing_in_other_software/ --- # What is a good way to save images for later processing in other software? diff --git a/faq/i_am_having_problems_printing_figures_that_use_opacity.md b/faq/figure_opacity.md similarity index 89% rename from faq/i_am_having_problems_printing_figures_that_use_opacity.md rename to faq/figure_opacity.md index d8137568a..6140bc20a 100644 --- a/faq/i_am_having_problems_printing_figures_that_use_opacity.md +++ b/faq/figure_opacity.md @@ -2,6 +2,8 @@ title: I am having problems printing figures that use opacity category: faq tags: [plotting] +redirect_from: + - /faq/i_am_having_problems_printing_figures_that_use_opacity/ --- # I am having problems printing figures that use opacity diff --git a/faq/how_can_i_extend_the_reading_functions_with_a_new_dataformat.md b/faq/fileio_dataformat.md similarity index 97% rename from faq/how_can_i_extend_the_reading_functions_with_a_new_dataformat.md rename to faq/fileio_dataformat.md index 2960c9147..34eeefa07 100644 --- a/faq/how_can_i_extend_the_reading_functions_with_a_new_dataformat.md +++ b/faq/fileio_dataformat.md @@ -2,6 +2,8 @@ title: How can I extend the reading functions with a new dataformat? category: faq tags: [dataformat, preprocessing] +redirect_from: + - /faq/how_can_i_extend_the_reading_functions_with_a_new_dataformat/ --- # How can I extend the reading functions with a new dataformat? diff --git a/faq/why_are_the_fileio_functions_stateless_does_the_fseek_not_make_them_very_slow.md b/faq/fileio_stateless.md similarity index 97% rename from faq/why_are_the_fileio_functions_stateless_does_the_fseek_not_make_them_very_slow.md rename to faq/fileio_stateless.md index b5d71a3c2..1a298baf0 100644 --- a/faq/why_are_the_fileio_functions_stateless_does_the_fseek_not_make_them_very_slow.md +++ b/faq/fileio_stateless.md @@ -2,6 +2,8 @@ title: Why are the fileio functions stateless, does the fseek not make them very slow? category: faq tags: [memory, matlab] +redirect_from: + - /faq/why_are_the_fileio_functions_stateless_does_the_fseek_not_make_them_very_slow/ --- # Why are the fileio functions stateless, does the fseek not make them very slow? diff --git a/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmconvol_in_ft_freqanalyis.md b/faq/freqanalysis_foimismatchmtmconvol.md similarity index 87% rename from faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmconvol_in_ft_freqanalyis.md rename to faq/freqanalysis_foimismatchmtmconvol.md index c2e704956..dab47382f 100644 --- a/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmconvol_in_ft_freqanalyis.md +++ b/faq/freqanalysis_foimismatchmtmconvol.md @@ -1,10 +1,13 @@ --- -title: Why does my output.freq not match my cfg.foi when using 'mtmconvol' in ft_freqanalyis? +title: Why does my output.freq not match my cfg.foi when using 'mtmconvol' in ft_freqanalysis? category: faq tags: [freq, mtmconvol] +redirect_from: + - /faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmconvol_in_ft_freqanalysis/ + - /faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmconvol_in_ft_freqanalyis/ --- -# Why does my output.freq not match my cfg.foi when using 'mtmconvol' in ft_freqanalyis? +# Why does my output.freq not match my cfg.foi when using 'mtmconvol' in ft_freqanalysis? Conceptually, a time frequency analysis can be thought of as a time domain convolution of a signal with a set of wavelets, each of these being designed to capture some feature in the data (i.e. the time dependent fluctuations of the amplitude (and phase) of band-limited signal components). To this end, the 'mtmconvol'-method uses sine/cosine waves, tapered with multitapers (or Hanning tapers). Computationally, the FieldTrip implementation uses the trick: "convolution in the time domain is equivalent to multiplication in the frequency domain". In other words, rather than convolving the time domain signal with the wavelets of different frequencies, the Fourier representation of the data is multiplied with the Fourier representation of the wavelets (and the inverse fourier transform is computed to get to the time domain representation again). This puts some constraints on the actual frequencies that can be returned by the algorithm. Specifically, only those frequency bins that are permitted by the inherent resolution determined by the length of the data (+potential zero-padding). Given a total length (data+zero padding) of T, which yields a frequency resolution of 1/T, FieldTrip will return the frequencies that are closest (but not necessarily equal to) the requested frequencies in cfg.foi. diff --git a/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmfft_in_ft_freqanalyis.md b/faq/freqanalysis_foimismatchmtmfft.md similarity index 77% rename from faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmfft_in_ft_freqanalyis.md rename to faq/freqanalysis_foimismatchmtmfft.md index 2b01ede3d..4040b2884 100644 --- a/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmfft_in_ft_freqanalyis.md +++ b/faq/freqanalysis_foimismatchmtmfft.md @@ -1,10 +1,13 @@ --- -title: Why does my output.freq not match my cfg.foi when using 'mtmfft' in ft_freqanalyis +title: Why does my output.freq not match my cfg.foi when using 'mtmfft' in ft_freqanalysis category: faq tags: [freq] +redirect_from: + - /faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmfft_in_ft_freqanalysis/ + - /faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmfft_in_ft_freqanalyis/ --- -# Why does my output.freq not match my cfg.foi when using 'mtmfft' in ft_freqanalyis +# Why does my output.freq not match my cfg.foi when using 'mtmfft' in ft_freqanalysis The length of your time window determines the spectral resolution. If you have a time window of 1 second, you will get 1 Hz resolution, i.e. you can get estimates of power at integer multiples of 1 Hz. If you have a time window of 1.5 second, you will get a frequency resolution of 1/1.5=0.6667 Hz. That means that you can estimate power at [0.6667 1.3333 2.0000 2.6667 ...] Hz. diff --git a/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis.md b/faq/freqanalysis_foimismatchwavelet.md similarity index 89% rename from faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis.md rename to faq/freqanalysis_foimismatchwavelet.md index d0d7a7dd4..de6b63a46 100644 --- a/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis.md +++ b/faq/freqanalysis_foimismatchwavelet.md @@ -1,10 +1,13 @@ --- -title: Why does my output.freq not match my cfg.foi when using 'wavelet' (formerly 'wltconvol') in ft_freqanalyis? +title: Why does my output.freq not match my cfg.foi when using 'wavelet' (formerly 'wltconvol') in ft_freqanalysis? category: faq tags: [freq, wavelet] +redirect_from: + - /faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalysis/ + - /faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis/ --- -# Why does my output.freq not match my cfg.foi when using 'wavelet' (formerly 'wltconvol') in ft_freqanalyis? +# Why does my output.freq not match my cfg.foi when using 'wavelet' (formerly 'wltconvol') in ft_freqanalysis? Conceptually, a wavelet analysis is a time domain convolution of a signal with a set of wavelets, each of these being designed to capture some feature in the data. In neuroscience, we typically use Morlet-wavelets, which are designed to capture sine and cosine waves in the data. This is because a Morlet wavelet consists of a sine/cosine wave, tapered by a gaussian window. When doing a spectral decomposition, the goal typically is to assign the fluctuations in the signal to distinct frequency bands. Importantly, the (implicitly) required behavior of the spectral transformation is, that the power estimated at X Hz truly comes from signal fluctuations at X Hz., and not from signal fluctuations at Y Hz. (and Z Hz etc). This is the issue of spectral leakage, and a few signal processing tricks are needed to optimally control for this. In the context of wavelet analysis in FieldTrip and in order to minimize detrimental effects of (unpredictable spectral leakage), you need to keep 2 things in min diff --git a/faq/why_am_i_not_getting_exact_integer_frequencies.md b/faq/freqanalysis_foinoninteger.md similarity index 98% rename from faq/why_am_i_not_getting_exact_integer_frequencies.md rename to faq/freqanalysis_foinoninteger.md index 7545cbc99..43120f53b 100644 --- a/faq/why_am_i_not_getting_exact_integer_frequencies.md +++ b/faq/freqanalysis_foinoninteger.md @@ -2,6 +2,8 @@ title: Why am I not getting integer frequencies? category: faq tags: [preprocessing, freq] +redirect_from: + - /faq/why_am_i_not_getting_exact_integer_frequencies/ --- # Why am I not getting integer frequencies? diff --git a/faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmconvol_in_ft_freqanalyis.md b/faq/freqanalysis_mtmconvol_new.md similarity index 79% rename from faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmconvol_in_ft_freqanalyis.md rename to faq/freqanalysis_mtmconvol_new.md index 259d7f6aa..b86960da1 100644 --- a/faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmconvol_in_ft_freqanalyis.md +++ b/faq/freqanalysis_mtmconvol_new.md @@ -1,10 +1,13 @@ --- -title: What are the differences between the old and the new implementation of 'mtmconvol' in ft_freqanalyis? +title: What are the differences between the old and the new implementation of 'mtmconvol' in ft_freqanalysis? category: faq tags: [freq, mtmconvol] +redirect_from: + - /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmconvol_in_ft_freqanalysis/ + - /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmconvol_in_ft_freqanalyis/ --- -# What are the differences between the old and the new implementation of 'mtmconvol' in ft_freqanalyis? +# What are the differences between the old and the new implementation of 'mtmconvol' in ft_freqanalysis? Several things have changed in the new implementation of frequency analysis by the new low-level module 'specest'. diff --git a/faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmfft_in_ft_freqanalyis.md b/faq/freqanalysis_mtmfft_new.md similarity index 69% rename from faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmfft_in_ft_freqanalyis.md rename to faq/freqanalysis_mtmfft_new.md index c3ea0410b..9a4eae067 100644 --- a/faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmfft_in_ft_freqanalyis.md +++ b/faq/freqanalysis_mtmfft_new.md @@ -1,10 +1,13 @@ --- -title: What are the differences between the old and the new implementation of 'mtmftt' in ft_freqanalyis? +title: What are the differences between the old and the new implementation of 'mtmftt' in ft_freqanalysis? category: faq tags: [freq, mtmfft] +redirect_from: + - /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmfft_in_ft_freqanalysis/ + - /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmfft_in_ft_freqanalyis/ --- -# What are the differences between the old and the new implementation of 'mtmftt' in ft_freqanalyis? +# What are the differences between the old and the new implementation of 'mtmftt' in ft_freqanalysis? Several things have changed in the new implementation of frequency analysis by the new low-level module 'specest'. diff --git a/faq/what_does_padding_not_sufficient_for_requested_frequency_resolution_mean.md b/faq/freqanalysis_paddinginsufficient.md similarity index 94% rename from faq/what_does_padding_not_sufficient_for_requested_frequency_resolution_mean.md rename to faq/freqanalysis_paddinginsufficient.md index a63df1693..03245cb4c 100644 --- a/faq/what_does_padding_not_sufficient_for_requested_frequency_resolution_mean.md +++ b/faq/freqanalysis_paddinginsufficient.md @@ -2,6 +2,8 @@ title: What does "padding not sufficient for requested frequency resolution" mean? category: faq tags: [freq] +redirect_from: + - /faq/what_does_padding_not_sufficient_for_requested_frequency_resolution_mean/ --- # What does "padding not sufficient for requested frequency resolution" mean? diff --git a/faq/what_convention_is_used_to_define_absolute_phase_in_mtmconvol_wavelet_and_mtmfft.md b/faq/freqanalysis_phasedefinition.md similarity index 88% rename from faq/what_convention_is_used_to_define_absolute_phase_in_mtmconvol_wavelet_and_mtmfft.md rename to faq/freqanalysis_phasedefinition.md index 7e944f205..fcf1214b5 100644 --- a/faq/what_convention_is_used_to_define_absolute_phase_in_mtmconvol_wavelet_and_mtmfft.md +++ b/faq/freqanalysis_phasedefinition.md @@ -2,6 +2,8 @@ title: What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'? category: faq tags: [freq, mtmconvol, wavelet, mtmfft, phase] +redirect_from: + - /faq/what_convention_is_used_to_define_absolute_phase_in_mtmconvol_wavelet_and_mtmfft/ --- # What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'? diff --git a/faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_wavelet_formerly_wltconvol_in_ft_freqanalyis.md b/faq/freqanalysis_wavelet_new.md similarity index 76% rename from faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_wavelet_formerly_wltconvol_in_ft_freqanalyis.md rename to faq/freqanalysis_wavelet_new.md index 618bd0414..0cb45431a 100644 --- a/faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_wavelet_formerly_wltconvol_in_ft_freqanalyis.md +++ b/faq/freqanalysis_wavelet_new.md @@ -1,14 +1,17 @@ --- -title: What are the differences between the old and the new implementation of 'wavelet' (formerly 'wltconvol') in ft_freqanalyis? +title: What are the differences between the old and the new implementation of 'wavelet' (formerly 'wltconvol') in ft_freqanalysis? category: faq tags: [freq, wavelet] +redirect_from: + - /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_wavelet_formerly_wltconvol_in_ft_freqanalysis/ + - /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_wavelet_formerly_wltconvol_in_ft_freqanalyis/ --- -# What are the differences between the old and the new implementation of 'wavelet' (formerly 'wltconvol') in ft_freqanalyis? +# What are the differences between the old and the new implementation of 'wavelet' (formerly 'wltconvol') in ft_freqanalysis? Several things have changed in the new implementation of frequency analysis by the new low-level module 'specest'. - All output is now phase-shifted such that an angle of 0 of any fourier-coefficient always means a peak of an oscillation in the data, and an angle of pi/-pi will always mean the trough of an oscillation (wavelet wise angle = 0 is implemented as cosine at peak, and sine in up-going flank) -- 'wavelet' now uses an accurate frequency vector for building its wavelets (determined by fsample and nsample, with cfg.foi as starting point), instead of an uncorrected cfg.foi. In many cases this will cause frequencies like e.g., 4.0978 to show up in the output. This is not an _inaccuracy_, it is _more precise_ labeling of the frequency content. This means that it is _very important_ to make sure you _zero-pad datasets to an equal length_ (using cfg.padding) that you want to compare later on: the output-foi must be identical (more information can be found [here](/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis)). +- 'wavelet' now uses an accurate frequency vector for building its wavelets (determined by fsample and nsample, with cfg.foi as starting point), instead of an uncorrected cfg.foi. In many cases this will cause frequencies like e.g., 4.0978 to show up in the output. This is not an _inaccuracy_, it is _more precise_ labeling of the frequency content. This means that it is _very important_ to make sure you _zero-pad datasets to an equal length_ (using cfg.padding) that you want to compare later on: the output-foi must be identical (more information can be found [here](/faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalysis)). - The new implementation now correctly shifts the output by one single time-point compared to the old implementation. In the previous implementation, 'wltconvol', this was a sleeping bug. - cfg.method = 'fourier' is now an appropriate output. diff --git a/faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session.md b/faq/headlocalizer.md similarity index 98% rename from faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session.md rename to faq/headlocalizer.md index ec5626224..5650a41c8 100644 --- a/faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session.md +++ b/faq/headlocalizer.md @@ -2,6 +2,8 @@ title: How can I monitor a subject's head position during a MEG session? category: faq tags: [meg, realtime] +redirect_from: + - /faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session/ --- # How can I monitor a subject's head position during a MEG session? @@ -75,7 +77,7 @@ This can be achieved by marking the head position indicator (HPI) coil positions You can reposition to i.e. to a previous recording session by specifying cfg.template. Either by pointing to another dataset; e.g., cfg.template = 'subject01xxx.ds' (CTF275 systems only), or by pointing to a text file created by clicking the Update button during a previous recording session; e.g., cfg.template = '29-Apr-2013-xxx.txt' (CTF275 and Neuromag systems). -{% include image src="/assets/img/faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session/anims1.gif" width="600" %} +{% include image src="/assets/img/faq/headlocalizer/anims1.gif" width="600" %} _Figure 1: Top (left plot) and back view (right plot) of the subject's head. Nasion is represented by a triangular marker and both auricular points by circular markers. To aid the subject with repositioning, the real-time fiducial positions are color coded to indicate the distances to the targets (green `< 1.5 mm, orange < 3 mm, and red >` 3 mm). If all three markers are within limits, the head turns light blue (CTF only). Click on the image for the animation._ diff --git a/faq/how_can_i_visualize_a_localspheres_volume_conductor_model.md b/faq/headmodel_localspheres.md similarity index 95% rename from faq/how_can_i_visualize_a_localspheres_volume_conductor_model.md rename to faq/headmodel_localspheres.md index 92cc8e415..cdaace03e 100644 --- a/faq/how_can_i_visualize_a_localspheres_volume_conductor_model.md +++ b/faq/headmodel_localspheres.md @@ -2,6 +2,8 @@ title: How can I visualize a localspheres volume conductor model? category: faq tags: [headmodel, localspheres] +redirect_from: + - /faq/how_can_i_visualize_a_localspheres_volume_conductor_model/ --- # How can I visualize a localspheres volume conductor model? diff --git a/faq/why_does_my_eegheadmodel_look_funny.md b/faq/headmodel_meshingproblem.md similarity index 91% rename from faq/why_does_my_eegheadmodel_look_funny.md rename to faq/headmodel_meshingproblem.md index d54032b4c..c56228de3 100644 --- a/faq/why_does_my_eegheadmodel_look_funny.md +++ b/faq/headmodel_meshingproblem.md @@ -2,6 +2,8 @@ title: Why does my EEG headmodel look funny? category: faq tags: [headmodel] +redirect_from: + - /faq/why_does_my_eegheadmodel_look_funny/ --- # Why does my EEG headmodel look funny? @@ -28,7 +30,7 @@ The image on disk has an ugly aliasing artifact at the top, causing the standard ft_plot_mesh(bnd0(3), 'facecolor',[0.4 0.4 0.4]); view([0 0]); -{% include image src="/assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd0.png" width="350" %} +{% include image src="/assets/img/faq/headmodel_meshingproblem/bnd0.png" width="350" %} _Figure 1. Aliasing artifact at the top leads to horns_ @@ -49,7 +51,7 @@ Adjusting the settings for the segmentation is helpful in this case, but will no ft_plot_mesh(bnd(3), 'facecolor',[0.4 0.4 0.4]); view([0 0]); -{% include image src="/assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd1.png" width="350" %} +{% include image src="/assets/img/faq/headmodel_meshingproblem/bnd1.png" width="350" %} _Figure 2. Adjustment of segmentation parameters gets rid of the aliasing artifact_ @@ -82,7 +84,7 @@ that we don't need to account for that anymore. mri2.anatomy = mri2.anatomy.*blob; ft_sourceplot([], mri2); -{% include image src="/assets/img/faq/why_does_my_eegheadmodel_look_funny/inhomogeneity.png" width="350" %} +{% include image src="/assets/img/faq/headmodel_meshingproblem/inhomogeneity.png" width="350" %} _Figure 3. Inhomogeneous anatomical image_ @@ -102,7 +104,7 @@ The above already throws a warning that the segmentation is not star-shaped, whi ft_plot_mesh(bnd2(3), 'facecolor',[0.4 0.4 0.4]); view([90 0]); -{% include image src="/assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd2.png" width="350" %} +{% include image src="/assets/img/faq/headmodel_meshingproblem/bnd2.png" width="350" %} _Figure 4. Failed headmodel_ @@ -124,6 +126,6 @@ As mentioned above, the bias in the image can be corrected as follows: ft_plot_mesh(bnd3(3), 'facecolor',[0.4 0.4 0.4]); view([90 0]); -{% include image src="/assets/img/faq/why_does_my_eegheadmodel_look_funny/bnd3.png" width="350" %} +{% include image src="/assets/img/faq/headmodel_meshingproblem/bnd3.png" width="350" %} _Figure 4. Headmodel after inhomogeneity correction_ diff --git a/faq/why_does_my_ica_output_contain_complex_numbers.md b/faq/ica_complexvalues.md similarity index 96% rename from faq/why_does_my_ica_output_contain_complex_numbers.md rename to faq/ica_complexvalues.md index 2f61ea273..b7d41528d 100644 --- a/faq/why_does_my_ica_output_contain_complex_numbers.md +++ b/faq/ica_complexvalues.md @@ -2,6 +2,8 @@ title: Why does my ICA output contain complex numbers? category: faq tags: [ica] +redirect_from: + - /faq/why_does_my_ica_output_contain_complex_numbers --- # Why does my ICA output contain complex numbers? diff --git a/faq/i_used_ica_on_my_meg_data_from_before_2012_and_now_fieldtrip_crashes_why_is_that.md b/faq/ica_crash.md similarity index 89% rename from faq/i_used_ica_on_my_meg_data_from_before_2012_and_now_fieldtrip_crashes_why_is_that.md rename to faq/ica_crash.md index 1be6171f4..6e771711e 100644 --- a/faq/i_used_ica_on_my_meg_data_from_before_2012_and_now_fieldtrip_crashes_why_is_that.md +++ b/faq/ica_crash.md @@ -2,6 +2,8 @@ title: I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that? category: faq tags: [ica, data, crash] +redirect_from: + - /faq/i_used_ica_on_my_meg_data_from_before_2012_and_now_fieldtrip_crashes_why_is_that/ --- # I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that? diff --git a/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal.md b/faq/ica_rereference.md similarity index 92% rename from faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal.md rename to faq/ica_rereference.md index ab41d9075..234c94d6e 100644 --- a/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal.md +++ b/faq/ica_rereference.md @@ -2,6 +2,8 @@ title: Should I rereference prior to or after ICA for artifact removal? category: faq tags: [ica] +redirect_from: + - /faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/ --- # Should I rereference prior to or after ICA for artifact removal? @@ -22,19 +24,19 @@ ICA is often used as a means for artifact removal. In this case, certain indepen In the following, an illustration of the above, theoretical explanation is provided. First, we have computed the correlation between independent components obtained from rereferenced and non-rereferenced data (Fig 1). -{% include image src="/assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/correlation.png" width="400" %} +{% include image src="/assets/img/faq/ica_rereference/correlation.png" width="400" %} It can be seen that in each line of the correlation matrix there is one correlation value that is significantly larger than the rest. This means that each element in one set of ICs has a matching counterpart in the other set. This can be made clearer by rearranging the lines and columns of the correlation matrix such that 1.) the index of a certain component in one set matches the index of its counterpart in the other set and 2.) the indices are ordered according to the descending order of correlation values (Fig. 2). -{% include image src="/assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/correlation_sorted.png" width="400" %} +{% include image src="/assets/img/faq/ica_rereference/correlation_sorted.png" width="400" %} The dominant diagonal illustrates that the ICA is relatively invariant with respect to the rereferencing. In a next step, we randomly selected roughly half of the matching pairs from both sets of ICs, removed those and computed the inverse ICA. In Fig. 3 and Fig. 4 it can be seen, again, that the results obtained from the two strategies (i.e. the "clean data") are close to identical. -{% include image src="/assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/multiplot.png" width="400" %} +{% include image src="/assets/img/faq/ica_rereference/multiplot.png" width="400" %} -{% include image src="/assets/img/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal/singleplot_FC1.png" width="400" %} +{% include image src="/assets/img/faq/ica_rereference/singleplot_FC1.png" width="400" %} ## Code diff --git a/faq/how_can_i_inspect_the_electrode_impedances_of_my_data.md b/faq/impedancecheck.md similarity index 95% rename from faq/how_can_i_inspect_the_electrode_impedances_of_my_data.md rename to faq/impedancecheck.md index 1137fa0ff..1b1c49c31 100644 --- a/faq/how_can_i_inspect_the_electrode_impedances_of_my_data.md +++ b/faq/impedancecheck.md @@ -2,6 +2,8 @@ title: How can I inspect the electrode impedances of my data? category: faq tags: [eeg, electrode] +redirect_from: + - /faq/how_can_i_inspect_the_electrode_impedances_of_my_data/ --- # How can I inspect the electrode impedances of my data? @@ -98,4 +100,4 @@ Make a plot of the ''imp'' structure containing the impedance values using a cus % figure ft_topoplotER(cfg, imp) -{% include image src="/assets/img/faq/how_can_i_inspect_the_electrode_impedances_of_my_data/impedance.png" %} +{% include image src="/assets/img/faq/impedancecheck/impedance.png" %} diff --git a/faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data.md b/faq/inspect_events.md similarity index 95% rename from faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data.md rename to faq/inspect_events.md index b10cda273..31f65ad3c 100644 --- a/faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data.md +++ b/faq/inspect_events.md @@ -2,6 +2,8 @@ title: How can I find out what eventvalues and eventtypes there are in my data? category: faq tags: [preprocessing, raw, trigger, event, values, type, eventvalue, eventtype] +redirect_from: + - /faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data/ --- # How can I find out what eventvalues and eventtypes there are in my data? diff --git a/faq/how_can_i_visualize_the_different_geometrical_objects_that_are_needed_for_forward_and_inverse_computations.md b/faq/inspect_geometries.md similarity index 93% rename from faq/how_can_i_visualize_the_different_geometrical_objects_that_are_needed_for_forward_and_inverse_computations.md rename to faq/inspect_geometries.md index 4dc308e4e..05a2e1aec 100644 --- a/faq/how_can_i_visualize_the_different_geometrical_objects_that_are_needed_for_forward_and_inverse_computations.md +++ b/faq/inspect_geometries.md @@ -2,6 +2,8 @@ title: How can I visualize the different geometrical objects that are needed for forward and inverse computations? category: faq tags: [source, headmodel, inverse, warning] +redirect_from: + - /faq/how_can_i_visualize_the_different_geometrical_objects_that_are_needed_for_forward_and_inverse_computations/ --- # How can I visualize the different geometrical objects that are needed for forward and inverse computations? diff --git a/faq/how_can_i_determine_the_anatomical_label_of_a_source.md b/faq/label_lookup.md similarity index 99% rename from faq/how_can_i_determine_the_anatomical_label_of_a_source.md rename to faq/label_lookup.md index 2f31caaf1..d78f05881 100644 --- a/faq/how_can_i_determine_the_anatomical_label_of_a_source.md +++ b/faq/label_lookup.md @@ -2,6 +2,8 @@ title: How can I determine the anatomical label of a source or electrode? category: faq tags: [source] +redirect_from: + - /faq/how_can_i_determine_the_anatomical_label_of_a_source/ --- # How can I determine the anatomical label of a source or electrode? diff --git a/faq/how_do_i_construct_a_layout_file_for_the_plotting_functions.md b/faq/layout_creation.md similarity index 74% rename from faq/how_do_i_construct_a_layout_file_for_the_plotting_functions.md rename to faq/layout_creation.md index 6258c3f6e..5f0a6fa26 100644 --- a/faq/how_do_i_construct_a_layout_file_for_the_plotting_functions.md +++ b/faq/layout_creation.md @@ -2,6 +2,8 @@ title: How do I construct a layout file for the plotting functions? category: faq tags: [layout, plotting] +redirect_from: + - /faq/how_do_i_construct_a_layout_file_for_the_plotting_functions/ --- # How do I construct a layout file for the plotting functions? diff --git a/faq/what_is_the_format_of_the_layout_file_which_is_used_for_plotting.md b/faq/layout_fileformat.md similarity index 97% rename from faq/what_is_the_format_of_the_layout_file_which_is_used_for_plotting.md rename to faq/layout_fileformat.md index 14f12dd65..418b70317 100644 --- a/faq/what_is_the_format_of_the_layout_file_which_is_used_for_plotting.md +++ b/faq/layout_fileformat.md @@ -2,6 +2,8 @@ title: What is the format of the layout file which is used for plotting? category: faq tags: [layout, plotting] +redirect_from: + - /faq/what_is_the_format_of_the_layout_file_which_is_used_for_plotting/ --- # What is the format of the layout file which is used for plotting? diff --git a/faq/what_are_the_different_neuromag_and_yokogawa_layouts_good_for.md b/faq/layout_magandgrad.md similarity index 93% rename from faq/what_are_the_different_neuromag_and_yokogawa_layouts_good_for.md rename to faq/layout_magandgrad.md index 7eca1dc80..995ad144a 100644 --- a/faq/what_are_the_different_neuromag_and_yokogawa_layouts_good_for.md +++ b/faq/layout_magandgrad.md @@ -2,6 +2,8 @@ title: What are the different Neuromag/Elekta/Megin and Yokogawa layouts good for? category: faq tags: [layout, plotting] +redirect_from: + - /faq/what_are_the_different_neuromag_and_yokogawa_layouts_good_for/ --- # What are the different Neuromag/Elekta/Megin and Yokogawa layouts good for? diff --git a/faq/how_to_compile_matlab_code_into_stand-alone_executables.md b/faq/matlab_compile.md similarity index 95% rename from faq/how_to_compile_matlab_code_into_stand-alone_executables.md rename to faq/matlab_compile.md index cdf352469..5ec37bb57 100644 --- a/faq/how_to_compile_matlab_code_into_stand-alone_executables.md +++ b/faq/matlab_compile.md @@ -2,6 +2,8 @@ title: How to compile MATLAB code into stand-alone executables? category: faq tags: [qsub] +redirect_from: + - /faq/how_to_compile_matlab_code_into_stand-alone_executables/ --- # How to compile MATLAB code into stand-alone executables? diff --git a/faq/matlab_version_7.3_2006b_crashes_when_i_try_to_do.md b/faq/matlab_crash73.md similarity index 93% rename from faq/matlab_version_7.3_2006b_crashes_when_i_try_to_do.md rename to faq/matlab_crash73.md index ed00371dc..3eba352ef 100644 --- a/faq/matlab_version_7.3_2006b_crashes_when_i_try_to_do.md +++ b/faq/matlab_crash73.md @@ -2,6 +2,8 @@ title: MATLAB version 7.3 (2006b) crashes when I try to do ... category: faq tags: [matlab] +redirect_from: + - /faq/matlab_version_7.3_2006b_crashes_when_i_try_to_do/ --- # MATLAB version 7.3 (2006b) crashes when I try to do ... diff --git a/faq/how_can_i_debug_my_analysis_script_if_a_fieldtrip_function_gives_an_error.md b/faq/matlab_debugging.md similarity index 97% rename from faq/how_can_i_debug_my_analysis_script_if_a_fieldtrip_function_gives_an_error.md rename to faq/matlab_debugging.md index 32b5edfc7..4351ad0ab 100644 --- a/faq/how_can_i_debug_my_analysis_script_if_a_fieldtrip_function_gives_an_error.md +++ b/faq/matlab_debugging.md @@ -2,6 +2,8 @@ title: How can I debug my analysis script if a FieldTrip function gives an error? category: faq tags: [debug] +redirect_from: + - /faq/how_can_i_debug_my_analysis_script_if_a_fieldtrip_function_gives_an_error/ --- # How can I debug my analysis script if a FieldTrip function gives an error? diff --git a/faq/matlab_complains_about_a_missing_or_invalid_mex_file_what_should_i_do.md b/faq/matlab_mexinvalid.md similarity index 98% rename from faq/matlab_complains_about_a_missing_or_invalid_mex_file_what_should_i_do.md rename to faq/matlab_mexinvalid.md index b6930569d..d69d3f2ec 100644 --- a/faq/matlab_complains_about_a_missing_or_invalid_mex_file_what_should_i_do.md +++ b/faq/matlab_mexinvalid.md @@ -2,6 +2,8 @@ title: MATLAB complains about a missing or invalid mex file, what should I do? category: faq tags: [matlab, mex] +redirect_from: + - /faq/matlab_complains_about_a_missing_or_invalid_mex_file_what_should_i_do/ --- # MATLAB complains about a missing or invalid mex file, what should I do? diff --git a/faq/matlab_does_not_see_the_functions_in_the_private_directory.md b/faq/matlab_privatefunctions.md similarity index 94% rename from faq/matlab_does_not_see_the_functions_in_the_private_directory.md rename to faq/matlab_privatefunctions.md index 3b0ff9aa4..a50bd9c96 100644 --- a/faq/matlab_does_not_see_the_functions_in_the_private_directory.md +++ b/faq/matlab_privatefunctions.md @@ -2,6 +2,8 @@ title: MATLAB does not see the functions in the "private" directory category: faq tags: [function, matlab] +redirect_from: + - /faq/matlab_does_not_see_the_functions_in_the_private_directory/ --- # MATLAB does not see the functions in the "private" directory diff --git a/faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers.md b/faq/mergedata.md similarity index 96% rename from faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers.md rename to faq/mergedata.md index 5b80294ab..1c2fb9cce 100644 --- a/faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers.md +++ b/faq/mergedata.md @@ -2,6 +2,8 @@ title: How can I merge two datasets that were acquired simultaneously with different amplifiers? category: faq tags: [preprocessing, raw, dataformat, eeg, meg] +redirect_from: + - /faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers/ --- # How can I merge two datasets that were acquired simultaneously with different amplifiers? diff --git a/faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified.md b/faq/mex_osx.md similarity index 91% rename from faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified.md rename to faq/mex_osx.md index 036245e60..84f51e7fe 100644 --- a/faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified.md +++ b/faq/mex_osx.md @@ -2,6 +2,8 @@ title: MATLAB complains that mexmaci64 cannot be opened because the developer cannot be verified category: faq tags: [matlab, mex] +redirect_from: + - /faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified/ --- # MATLAB complains that mexmaci64 cannot be opened because the developer cannot be verified @@ -13,7 +15,7 @@ When you try to use FieldTrip on macOS Catalina or later, you may get an error l macOS cannot verify that this app is free from malware. ``` -{% include image src="/assets/img/faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified/screenshot.png" width="400" %} +{% include image src="/assets/img/faq/mex_osx/screenshot.png" width="400" %} or a similar error for another mex file that is included with FieldTrip. diff --git a/faq/why_are_there_multiple_neighbour_templates_for_the_neuromag306_system.md b/faq/neighbours_neuromag.md similarity index 89% rename from faq/why_are_there_multiple_neighbour_templates_for_the_neuromag306_system.md rename to faq/neighbours_neuromag.md index 606bd80b2..1ed1d4aed 100644 --- a/faq/why_are_there_multiple_neighbour_templates_for_the_neuromag306_system.md +++ b/faq/neighbours_neuromag.md @@ -2,6 +2,8 @@ title: Why are there multiple neighbour templates for the Neuromag306 system? category: faq tags: [neuromag, template, warning] +redirect_from: + - /faq/why_are_there_multiple_neighbour_templates_for_the_neuromag306_system/ --- # Why are there multiple neighbour templates for the Neuromag306 system? diff --git a/faq/how_does_ft_prepare_neighbours_work.md b/faq/neighbours_prepare.md similarity index 98% rename from faq/how_does_ft_prepare_neighbours_work.md rename to faq/neighbours_prepare.md index 9a0bdf5ec..0e025ffd6 100644 --- a/faq/how_does_ft_prepare_neighbours_work.md +++ b/faq/neighbours_prepare.md @@ -2,6 +2,8 @@ title: How does ft_prepare_neighbours work? category: faq tags: [statistics, cluster] +redirect_from: + - /faq/how_does_ft_prepare_neighbours_work/ --- # How does ft_prepare_neighbours work? diff --git a/faq/how_can_i_visualize_the_neuromag_head_position_indicator_coils.md b/faq/neuromag_hpi.md similarity index 95% rename from faq/how_can_i_visualize_the_neuromag_head_position_indicator_coils.md rename to faq/neuromag_hpi.md index 6c630c37a..9af1b4844 100644 --- a/faq/how_can_i_visualize_the_neuromag_head_position_indicator_coils.md +++ b/faq/neuromag_hpi.md @@ -2,6 +2,8 @@ title: How can I visualize the neuromag head position indicator coils? category: faq tags: [neuromag, head, localization] +redirect_from: + - /faq/how_can_i_visualize_the_neuromag_head_position_indicator_coils/ --- # How can I visualize the neuromag head position indicator coils? @@ -80,4 +82,4 @@ Note that in this example dataset, the digitized position of HPI coil 5, energiz cfg.coilfreq = [293, 307, 314, 321]; % note 328 Hz is missing -{% include image src="/assets/img/faq/how_can_i_visualize_the_neuromag_head_position_indicator_coils/neuromag_wikiexample.png" width="400" %} +{% include image src="/assets/img/faq/neuromag_hpi/neuromag_wikiexample.png" width="400" %} diff --git a/faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this.md b/faq/neuroscan.md similarity index 90% rename from faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this.md rename to faq/neuroscan.md index 0504a17d3..3a8c8e6cf 100644 --- a/faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this.md +++ b/faq/neuroscan.md @@ -2,6 +2,8 @@ title: I have problems reading in neuroscan .cnt files. How can I fix this? category: faq tags: [raw, neuroscan, eeg, dataformat, preprocessing] +redirect_from: + - /faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this/ --- # I have problems reading in neuroscan .cnt files. How can I fix this? diff --git a/faq/can_i_use_octave_instead_of_matlab.md b/faq/octave.md similarity index 95% rename from faq/can_i_use_octave_instead_of_matlab.md rename to faq/octave.md index 71441d9ce..7d7facaae 100644 --- a/faq/can_i_use_octave_instead_of_matlab.md +++ b/faq/octave.md @@ -2,6 +2,8 @@ title: Can I use Octave instead of MATLAB? category: faq tags: [octave] +redirect_from: + - /faq/can_i_use_octave_instead_of_matlab/ --- # Can I use Octave instead of MATLAB? diff --git a/faq/i_am_getting_strange_artifacts_in_figures_that_use_opacity.md b/faq/opacityrendering.md similarity index 94% rename from faq/i_am_getting_strange_artifacts_in_figures_that_use_opacity.md rename to faq/opacityrendering.md index de73023fa..852e7e4f8 100644 --- a/faq/i_am_getting_strange_artifacts_in_figures_that_use_opacity.md +++ b/faq/opacityrendering.md @@ -2,6 +2,8 @@ title: I am getting strange artifacts in figures that use opacity category: faq tags: [plotting, artifact] +redirect_from: + - /faq/i_am_getting_strange_artifacts_in_figures_that_use_opacity/ --- # I am getting strange artifacts in figures that use opacity diff --git a/faq/how_do_i_install_the_openmeeg_binaries.md b/faq/openmeeg.md similarity index 98% rename from faq/how_do_i_install_the_openmeeg_binaries.md rename to faq/openmeeg.md index ad754e4de..ddb952015 100644 --- a/faq/how_do_i_install_the_openmeeg_binaries.md +++ b/faq/openmeeg.md @@ -2,6 +2,8 @@ title: How do I install the OpenMEEG binaries category: faq tags: [openmeeg, headmodel] +redirect_from: + - /faq/how_do_i_install_the_openmeeg_binaries/ --- # How do I install the OpenMEEG binaries diff --git a/faq/how_to_interpret_the_sign_of_the_phase_slope_index.md b/faq/phaseslopeindex.md similarity index 96% rename from faq/how_to_interpret_the_sign_of_the_phase_slope_index.md rename to faq/phaseslopeindex.md index 59bfb7a1c..bb049a778 100644 --- a/faq/how_to_interpret_the_sign_of_the_phase_slope_index.md +++ b/faq/phaseslopeindex.md @@ -2,6 +2,8 @@ title: How to interpret the sign of the phase slope index? category: faq tags: [coherence] +redirect_from: + - /faq/how_to_interpret_the_sign_of_the_phase_slope_index/ --- # How to interpret the sign of the phase slope index? diff --git a/faq/how_can_i_process_continuous_data_without_triggers.md b/faq/preproc_continuous.md similarity index 97% rename from faq/how_can_i_process_continuous_data_without_triggers.md rename to faq/preproc_continuous.md index f29c1ad9a..bfad7be5e 100644 --- a/faq/how_can_i_process_continuous_data_without_triggers.md +++ b/faq/preproc_continuous.md @@ -2,6 +2,8 @@ title: How can I process continuous data without triggers? category: faq tags: [preprocessing, continuous, raw] +redirect_from: + - /faq/how_can_i_process_continuous_data_without_triggers/ --- # How can I process continuous data without triggers? diff --git a/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.md b/faq/preproc_downsample.md similarity index 91% rename from faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.md rename to faq/preproc_downsample.md index 3e74a8fce..7030301a0 100644 --- a/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.md +++ b/faq/preproc_downsample.md @@ -2,6 +2,8 @@ title: How can I preprocess a dataset that is too large to fit into memory? category: faq tags: [preprocessing, memory] +redirect_from: + - /faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory/ --- # How can I preprocess a dataset that is too large to fit into memory? diff --git a/faq/what_kind_of_filters_can_i_apply_to_my_data.md b/faq/preproc_filtertypes.md similarity index 93% rename from faq/what_kind_of_filters_can_i_apply_to_my_data.md rename to faq/preproc_filtertypes.md index 567636eed..e153b3907 100644 --- a/faq/what_kind_of_filters_can_i_apply_to_my_data.md +++ b/faq/preproc_filtertypes.md @@ -2,6 +2,8 @@ title: What kind of filters can I apply to my data? category: faq tags: [preprocessing, timelock, freq, artifact, filter] +redirect_from: + - /faq/what_kind_of_filters_can_i_apply_to_my_data/ --- # What kind of filters can I apply to my data? diff --git a/faq/how_does_the_filter_padding_in_preprocessing_work.md b/faq/preproc_padding.md similarity index 81% rename from faq/how_does_the_filter_padding_in_preprocessing_work.md rename to faq/preproc_padding.md index cc6e900eb..552ec001a 100644 --- a/faq/how_does_the_filter_padding_in_preprocessing_work.md +++ b/faq/preproc_padding.md @@ -2,6 +2,8 @@ title: How does the filter padding in preprocessing work? category: faq tags: [preprocessing, artifact, filter] +redirect_from: + - /faq/how_does_the_filter_padding_in_preprocessing_work/ --- # How does the filter padding in preprocessing work? @@ -10,4 +12,4 @@ The preprocessing parameter _cfg.padding_ defines the duration to which the data Padding the data can be beneficial, since the edge artifacts that are typically seen after filtering will be in the padding and not in the segment of interest. Padding is also relevant for DFT filtering of the 50Hz line noise artifact: long padding ensures a higher frequency resolution for the DFT filter, causing a narrower notch to be removed from the data. This is especially relevant for multi-taper frequency analyses. -See also this [FAQ](/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts) on how the different types of padding are to be interpreted in relation to artifact detection. +See also this [FAQ](/faq/artifact_padding) on how the different types of padding are to be interpreted in relation to artifact detection. diff --git a/faq/why_are_so_many_of_the_interesting_functions_in_the_private_directories.md b/faq/privatefunctions_why.md similarity index 94% rename from faq/why_are_so_many_of_the_interesting_functions_in_the_private_directories.md rename to faq/privatefunctions_why.md index 8fbfab09d..5fcb94406 100644 --- a/faq/why_are_so_many_of_the_interesting_functions_in_the_private_directories.md +++ b/faq/privatefunctions_why.md @@ -2,6 +2,8 @@ title: Why are so many of the interesting functions in the private directories? category: faq tags: [function, matlab] +redirect_from: + - /faq/why_are_so_many_of_the_interesting_functions_in_the_private_directories/ --- # Why are so many of the interesting functions in the private directories? diff --git a/faq/how_can_i_use_my_macbook_pro_for_stimulus_presentation_in_the_meg_lab.md b/faq/psychtoolbox_macbook.md similarity index 94% rename from faq/how_can_i_use_my_macbook_pro_for_stimulus_presentation_in_the_meg_lab.md rename to faq/psychtoolbox_macbook.md index 02b7c3747..92a441aab 100644 --- a/faq/how_can_i_use_my_macbook_pro_for_stimulus_presentation_in_the_meg_lab.md +++ b/faq/psychtoolbox_macbook.md @@ -2,6 +2,8 @@ title: How can I use my MacBook Pro for stimulus presentation in the MEG lab? category: faq tags: [matlab] +redirect_from: + - /faq/how_can_i_use_my_macbook_pro_for_stimulus_presentation_in_the_meg_lab/ --- # How can I use my MacBook Pro for stimulus presentation in the MEG lab? diff --git a/faq/is_it_important_to_have_accurate_measurements_of_electrode_locations_for_eeg_source_reconstruction.md b/faq/sensors_accuracy.md similarity index 90% rename from faq/is_it_important_to_have_accurate_measurements_of_electrode_locations_for_eeg_source_reconstruction.md rename to faq/sensors_accuracy.md index b5ff19510..6a6a4a96d 100644 --- a/faq/is_it_important_to_have_accurate_measurements_of_electrode_locations_for_eeg_source_reconstruction.md +++ b/faq/sensors_accuracy.md @@ -2,6 +2,8 @@ title: Is it important to have accurate measurements of electrode locations for EEG source reconstruction? category: faq tags: [source, eeg] +redirect_from: + - /faq/is_it_important_to_have_accurate_measurements_of_electrode_locations_for_eeg_source_reconstruction/ --- # Is it important to have accurate measurements of electrode locations for EEG source reconstruction? diff --git a/faq/how_are_electrodes_magnetometers_or_gradiometers_described.md b/faq/sensors_definition.md similarity index 99% rename from faq/how_are_electrodes_magnetometers_or_gradiometers_described.md rename to faq/sensors_definition.md index d3bf7b461..0493c504b 100644 --- a/faq/how_are_electrodes_magnetometers_or_gradiometers_described.md +++ b/faq/sensors_definition.md @@ -2,6 +2,8 @@ title: How are electrodes, magnetometers or gradiometers described? category: faq tags: [electrode, eeg, meg, fiducial, layout] +redirect_from: + - /faq/how_are_electrodes_magnetometers_or_gradiometers_described/ --- # How are electrodes, magnetometers or gradiometers described? diff --git a/faq/how_can_i_define_neighbouring_sensors.md b/faq/sensors_neighbours.md similarity index 98% rename from faq/how_can_i_define_neighbouring_sensors.md rename to faq/sensors_neighbours.md index 49efae746..4ec199e9d 100644 --- a/faq/how_can_i_define_neighbouring_sensors.md +++ b/faq/sensors_neighbours.md @@ -4,6 +4,7 @@ category: faq tags: [statistics, cluster, plotting] redirect_from: - /faq/how_can_i_define_my_own_neighbourhood_template/ + - /faq/how_can_i_define_neighbouring_sensors/ --- # How can I define neighbouring sensors? diff --git a/faq/how_can_i_test_the_serial_port_connection_between_two_computers.md b/faq/serialport.md similarity index 95% rename from faq/how_can_i_test_the_serial_port_connection_between_two_computers.md rename to faq/serialport.md index e9b863925..332400867 100644 --- a/faq/how_can_i_test_the_serial_port_connection_between_two_computers.md +++ b/faq/serialport.md @@ -2,6 +2,8 @@ title: What kind of cable do I need for a serial port connection between two computers? category: faq tags: [realtime] +redirect_from: + - /faq/how_can_i_test_the_serial_port_connection_between_two_computers/ --- # What kind of cable do I need for a serial port connection between two computers? @@ -77,7 +79,7 @@ This is what I did on my office PC using FieldTrip commands **[ft_read_event](/r What I got looks like this: -{% include image src="/assets/img/faq/how_can_i_test_the_serial_port_connection_between_two_computers/serial_connect_write_read_event.jpg" width="400" %} +{% include image src="/assets/img/faq/serialport/serial_connect_write_read_event.jpg" width="400" %} Alternatively, one can simply use MATLAB serial objects and low-level reading function fread or fscan @@ -154,4 +156,4 @@ Alternatively, one can simply use MATLAB serial objects and low-level reading fu The picture looks similar, only slightly faster. -{% include image src="/assets/img/faq/how_can_i_test_the_serial_port_connection_between_two_computers/serial_connect_write_read_matlab_serial.jpg" width="400" %} +{% include image src="/assets/img/faq/serialport/serial_connect_write_read_matlab_serial.jpg" width="400" %} diff --git a/faq/how_do_i_prevent_fieldtrip_from_printing_the_time_and_memory_after_each_function_call.md b/faq/showcallinfo.md similarity index 94% rename from faq/how_do_i_prevent_fieldtrip_from_printing_the_time_and_memory_after_each_function_call.md rename to faq/showcallinfo.md index a6742cbf4..f954a6183 100644 --- a/faq/how_do_i_prevent_fieldtrip_from_printing_the_time_and_memory_after_each_function_call.md +++ b/faq/showcallinfo.md @@ -2,6 +2,8 @@ title: How do I prevent FieldTrip from printing the time and memory after each function call? category: faq tags: [matlab] +redirect_from: + - /faq/how_do_i_prevent_fieldtrip_from_printing_the_time_and_memory_after_each_function_call/ --- # How do I prevent FieldTrip from printing the time and memory after each function call? diff --git a/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template.md b/faq/sourcemodel_deformation.md similarity index 87% rename from faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template.md rename to faq/sourcemodel_deformation.md index 325344648..d5df76c27 100755 --- a/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template.md +++ b/faq/sourcemodel_deformation.md @@ -2,6 +2,8 @@ title: Why is the source model deformed or incorrectly aligned after warping template? category: faq tags: [sourcemodel, mri, normalization] +redirect_from: + - /faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/ --- # Why is the source model deformed or incorrectly aligned after warping template? @@ -15,13 +17,13 @@ The procedure requires estimating a transformation between the subject's anatomy ft_plot_headmodel(headmodel, 'edgecolor', 'none', 'facealpha', 0.4,'facecolor', 'b'); ft_plot_mesh(sourcespace.pos(sourcespace.inside,:)); -{% include image src="/assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/sourcespace.png" %} +{% include image src="/assets/img/faq/sourcemodel_deformation/sourcespace.png" %} You can see that the source points are not well contained withing the head model. As a consequence, activity will be estimated outside the subject's head. Be aware that - once the source model coordinates are set back to the template coordinates - it will look as if there are no errors. The template source model will align perfectly with the template anatomy, it is just the estimated activity that will appear on the wrong place. The error stems from the warping of the template MRI to the individual subject's MRI. To transform the template to the subject's anatomy, **[ft_prepare_sourcemodel](/reference/ft_prepare_sourcemodel)** first does a normalization of the individual subject's MRI to the template, this gives a transformation matrix. It then inverts this transformation and applies it to the template grid. Therefore, if the normalization goes wrong, or finds a sub-optimal solution, it will create a bad inverted transformation and apply it to the template source model. We have seen this happening due to from sub-optimal anatomical MRIs, e.g., without proper contrast normalization, or with MRI scans where parts of the head are outside the field of view. An example is shown below: -{% include image src="/assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/bad_mri.png" %} +{% include image src="/assets/img/faq/sourcemodel_deformation/bad_mri.png" %} When you observe a inverse warped template grid that is weird, you can do a "manual" normalization with **[ft_volumenormalise](/reference/ft_volumenormalise)** to see if it is due to normalization errors. @@ -36,7 +38,7 @@ When you observe a inverse warped template grid that is weird, you can do a "man cfg.paramter = 'anatomy'; ft_sourceplot(cfg, mri_spm8) -{% include image src="/assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/Cronenberg.png" %} +{% include image src="/assets/img/faq/sourcemodel_deformation/Cronenberg.png" %} {% include markup/skyblue %} In early 2020 we switched the default SPM version used by FieldTrip from SPM8 to SPM12. @@ -58,7 +60,7 @@ The solution is to normalize MRIs with `cfg.spmversion = 'spm12'` and add `cfg.s cfg.paramter = 'anatomy'; ft_sourceplot(cfg, mri_spm12) -{% include image src="/assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/fixed_mri.png" %} +{% include image src="/assets/img/faq/sourcemodel_deformation/fixed_mri.png" %} You should add these configuration options to the `cfg` structure when calling **[ft_prepare_sourcemodel](/reference/ft_prepare_sourcemodel)**. These options will be passed on to **[ft_volumenormalise](/reference/ft_volumenormalise)**. Do note that the new SPM12 method is much slower than the old method. @@ -81,6 +83,6 @@ Inspect the warped source model as before: ft_plot_headmodel(headmodel, 'edgecolor', 'none', 'facealpha', 0.4,'facecolor','b'); ft_plot_mesh(sourcespace.pos(sourcespace.inside,:)); -{% include image src="/assets/img/faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template/sourcespace_fixed.png" %} +{% include image src="/assets/img/faq/sourcemodel_deformation/sourcespace_fixed.png" %} As an alternative you can consider using **[ft_volumebiascorrect](/reference/ft_volumebiascorrect)**. diff --git a/faq/how_can_i_map_source_locations_between_two_different_representations.md b/faq/sourcerecon_atlas.md similarity index 92% rename from faq/how_can_i_map_source_locations_between_two_different_representations.md rename to faq/sourcerecon_atlas.md index 135b56af7..65dc26882 100644 --- a/faq/how_can_i_map_source_locations_between_two_different_representations.md +++ b/faq/sourcerecon_atlas.md @@ -1,7 +1,9 @@ --- title: How can I map source locations onto an anatomical label in an atlas? category: faq -tags: [source, interpolate, atlas, label] +redirect_from: + - /faq/how_can_i_map_source_locations_between_two_different_representations/ + --- # How can I map source locations onto an anatomical label in an atlas? @@ -28,7 +30,7 @@ _Some useful tips:_ - Ensure that the units are consistent in atlas and sourcemodel. If that's not the case, use **[ft_convert_units](/reference/forward/ft_convert_units)**. - When using **[ft_read_atlas](/reference/fileio/ft_read_atlas)**, it is better to use an atlas defined in MNI space, like the AAL atlas, in order to avoid too much distortion when converting between MNI and Talairach space. The figure below exemplifies this issue. - {% include image src="/assets/img/faq/how_can_i_map_source_locations_between_two_different_representations/atlas_afni_brainweb_sourcespace.png" width="600" %} + {% include image src="/assets/img/faq/sourcerecon_atlas/atlas_afni_brainweb_sourcespace.png" width="600" %} _Comparing grey matter tagging using atlases AFNI (all labels; blue) and Brainweb (tissue grey_matter; red). Note how the AFNI version does not fill the volume conductor model completely, probably due to TAL to MNI transformation issues._ From the previous step, a field 'tissue' should be created in sourcemodel2: 'tissue' represents the anatomical labels, according to the corresponding atlas. 'atlas.tissuelabel' gives the labels that correspond to the numbers in the tissue field. diff --git a/faq/why_should_i_use_an_average_reference_for_eeg_source_reconstruction.md b/faq/sourcerecon_avgref.md similarity index 95% rename from faq/why_should_i_use_an_average_reference_for_eeg_source_reconstruction.md rename to faq/sourcerecon_avgref.md index 907aed73f..b827ce76e 100644 --- a/faq/why_should_i_use_an_average_reference_for_eeg_source_reconstruction.md +++ b/faq/sourcerecon_avgref.md @@ -1,7 +1,9 @@ --- title: Why should I use an average reference for EEG source reconstruction? category: faq -tags: [eeg, reference, source] +tags: [eeg, reference, source] +redirect_from: + - /faq/why_should_i_use_an_average_reference_for_eeg_source_reconstruction/ --- # Why should I use an average reference for EEG source reconstruction? diff --git a/faq/how_can_i_check_whether_the_grid_that_i_have_is_aligned_to_the_segmented_volume_and_to_the_sensor_gradiometer.md b/faq/sourcerecon_checkalignment.md similarity index 77% rename from faq/how_can_i_check_whether_the_grid_that_i_have_is_aligned_to_the_segmented_volume_and_to_the_sensor_gradiometer.md rename to faq/sourcerecon_checkalignment.md index 5160a7614..c44c5e952 100644 --- a/faq/how_can_i_check_whether_the_grid_that_i_have_is_aligned_to_the_segmented_volume_and_to_the_sensor_gradiometer.md +++ b/faq/sourcerecon_checkalignment.md @@ -2,6 +2,8 @@ title: How can I check whether the grid that I have is aligned to the segmented volume and to the sensor gradiometer? category: faq tags: [source, headmodel, seg] +redirect_from: + - /faq/how_can_i_check_whether_the_grid_that_i_have_is_aligned_to_the_segmented_volume_and_to_the_sensor_gradiometer/ --- # How can I check whether the grid that I have is aligned to the segmented volume and to the sensor gradiometer? @@ -9,6 +11,6 @@ tags: [source, headmodel, seg] Having a source model (i.e., positions of the dipoles), a head model (i.e., volume conduction model of the head), and the 'grad' structure, (i.e., information of the gradiometers) you can use the following: hold on - plot3(sourcemodel.pos(:,1), sourcemodel.pos(:,2), sourcemodel.pos(:,3),'.'); + ft_plot_mesh(sourcemodel); ft_plot_headmodel(headmodel); ft_plot_sens(grad); diff --git a/faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter.md b/faq/sourcerecon_greymatter.md similarity index 96% rename from faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter.md rename to faq/sourcerecon_greymatter.md index 75308b474..f99c02463 100644 --- a/faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter.md +++ b/faq/sourcerecon_greymatter.md @@ -2,6 +2,8 @@ title: Can I restrict the source reconstruction to the grey matter? category: faq tags: [source, mri, headmodel] +redirect_from: + - /faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter/ --- # Can I restrict the source reconstruction to the grey matter? diff --git a/faq/can_i_do_combined_eeg_and_meg_source_reconstruction.md b/faq/sourcerecon_meeg.md similarity index 93% rename from faq/can_i_do_combined_eeg_and_meg_source_reconstruction.md rename to faq/sourcerecon_meeg.md index 11de1e7b2..f45162f76 100644 --- a/faq/can_i_do_combined_eeg_and_meg_source_reconstruction.md +++ b/faq/sourcerecon_meeg.md @@ -2,6 +2,8 @@ title: Can I do combined EEG and MEG source reconstruction? category: faq tags: [eeg, meg, headmodel, source] +redirect_from: + - /faq/can_i_do_combined_eeg_and_meg_source_reconstruction/ --- # Can I do combined EEG and MEG source reconstruction? diff --git a/faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed.md b/faq/sourcerecon_outside.md similarity index 90% rename from faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed.md rename to faq/sourcerecon_outside.md index 29774d991..e78b7efca 100644 --- a/faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed.md +++ b/faq/sourcerecon_outside.md @@ -2,6 +2,8 @@ title: Is it good or bad to have dipole locations outside of the brain for which the source reconstruction is computed? category: faq tags: [source] +redirect_from: + - /faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed/ --- # Is it good or bad to have dipole locations outside of the brain for which the source reconstruction is computed? @@ -17,7 +19,7 @@ If the answer the first question is 'Yes', then it can be harmful. If the answer In this case, the head and source models are created with the intent of using a beamformer-type source reconstruction. As indicated by the red dots in the figure below, there are many dipoles for which the source reconstruction will be performed (i.e. they are labeled as 'inside'), but which do not fall inside the head. The source estimate at these location is interesting, because they can be used to identify e.g., muscle activity. Muscle activity in muscles at the back of the head would show increasing power towards the back of the brain, and will continue to increase in power passed the skull boundary. If power at these out-of-brain locations is not reconstructed, then it (muscle activity) could mistakingly be interpreted as activity in primary visual areas. -{% include image src="/assets/img/faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed/singleshelldipolelocations.png" width="400" %} +{% include image src="/assets/img/faq/sourcerecon_outside/singleshelldipolelocations.png" width="400" %} _Dipole locations of a source model plotted with on top of a singleshell head model. Dipole locations marked as 'inside' are red, dipole locations marked as 'outside' are blue._ @@ -25,7 +27,7 @@ _Dipole locations of a source model plotted with on top of a singleshell head mo In this example, a single sphere is used as a head model. The brain however, is not spherical. If we want to prevent brain areas to be missed in source reconstruction, a sphere is needed with a radius that is at least equal to the longest distance between any two points in the brain. Such a situation is depicted in the figure below. Here, the sphere is large enough to encompass the entire brain, and will therefore have many dipole locations which are not inside the brain (e.g., near temporal cortex). -{% include image src="/assets/img/faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed/singlespheredipolelocations.png" %} +{% include image src="/assets/img/faq/sourcerecon_outside/singlespheredipolelocations.png" %} _Dipole locations of a source model plotted with on top of a 'singlesphere' head model. Inside the sphere, the 'singleshell' head model in the above figure is plotted as well, to indicate the shape of the brain inside the sphere. Dipole locations marked as 'inside' are red, dipole locations marked as 'outside' are blue._ diff --git a/faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed.md b/faq/sourcerecon_rim.md similarity index 86% rename from faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed.md rename to faq/sourcerecon_rim.md index ae1c27cce..aa023c57e 100644 --- a/faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed.md +++ b/faq/sourcerecon_rim.md @@ -2,6 +2,8 @@ title: Why is there a rim around the brain for which the source reconstruction is not computed? category: faq tags: [source] +redirect_from: + - /faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed/ --- # Why is there a rim around the brain for which the source reconstruction is not computed? @@ -10,11 +12,11 @@ The **[ft_prepare_sourcemodel](/reference/ft_prepare_sourcemodel)** function sta Depending on the resolution of your 3-D grid, there will be points in the grid that _just_ ly outside the brain, i.e. close to those points there will be no points inside the brain that are included in the source reconstruction (see figure below). This results in a rim around the brain in which the source reconstruction is not performed, and hence no functional source data will be displayed in that rim after interpolating the source data onto the anatomical MRI. -{% include image src="/assets/img/faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed/grid_resolution_high.png" %} +{% include image src="/assets/img/faq/sourcerecon_rim/grid_resolution_high.png" %} If you have a low grid resolution, the rim will appear to be wider (see figure below). -{% include image src="/assets/img/faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed/grid_resolution_low.png" %} +{% include image src="/assets/img/faq/sourcerecon_rim/grid_resolution_low.png" %} In the figures, the brain is indicated with the circle, the "inside" points are indicated with red dots and the yellow region indicates that part of the brain volume on which the functional data will be interpolated. diff --git a/faq/how_to_select_the_correct_spm_toolbox.md b/faq/spmversion.md similarity index 96% rename from faq/how_to_select_the_correct_spm_toolbox.md rename to faq/spmversion.md index 3809aa06c..1f2b6d1fe 100644 --- a/faq/how_to_select_the_correct_spm_toolbox.md +++ b/faq/spmversion.md @@ -2,6 +2,8 @@ title: How to select the correct SPM toolbox? category: faq tags: [spm, mex, toolbox, path] +redirect_from: + - /faq/how_to_select_the_correct_spm_toolbox/ --- # How to select the correct SPM toolbox? diff --git a/faq/how_does_a_difference_in_trial_numbers_per_condition_affect_my_statistical_test.md b/faq/statistics_ntrials.md similarity index 97% rename from faq/how_does_a_difference_in_trial_numbers_per_condition_affect_my_statistical_test.md rename to faq/statistics_ntrials.md index f7612af0a..fb6baec33 100644 --- a/faq/how_does_a_difference_in_trial_numbers_per_condition_affect_my_statistical_test.md +++ b/faq/statistics_ntrials.md @@ -2,6 +2,8 @@ title: How does a difference in trial numbers per condition affect my statistical test category: faq tags: [statistics] +redirect_from: + - /faq/how_does_a_difference_in_trial_numbers_per_condition_affect_my_statistical_test/ --- {% include markup/red %} diff --git a/faq/what_is_the_idea_behind_statistical_inference_at_the_second-level.md b/faq/statistics_secondlevel.md similarity index 96% rename from faq/what_is_the_idea_behind_statistical_inference_at_the_second-level.md rename to faq/statistics_secondlevel.md index d487ee285..9b49808d5 100644 --- a/faq/what_is_the_idea_behind_statistical_inference_at_the_second-level.md +++ b/faq/statistics_secondlevel.md @@ -2,6 +2,8 @@ title: What is the idea behind statistical inference at the second-level? category: faq tags: [statistics, cluster] +redirect_from: + - /faq/what_is_the_idea_behind_statistical_inference_at_the_second-level/ --- # What is the idea behind statistical inference at the second-level? diff --git a/faq/why_is_fieldtrip_maintained_in_svn_and_not_in_git.md b/faq/svnversusgit.md similarity index 89% rename from faq/why_is_fieldtrip_maintained_in_svn_and_not_in_git.md rename to faq/svnversusgit.md index d095fdf45..8c0142ea6 100644 --- a/faq/why_is_fieldtrip_maintained_in_svn_and_not_in_git.md +++ b/faq/svnversusgit.md @@ -2,6 +2,8 @@ title: Why was FieldTrip maintained in SVN and not in Git? category: faq tags: [development, cvs, svn, git] +redirect_from: + - /faq/why_is_fieldtrip_maintained_in_svn_and_not_in_git/ --- # Why was FieldTrip maintained in SVN and not in Git? diff --git a/faq/how_can_i_do_time-frequency_analysis_on_continuous_data.md b/faq/tfr_continuous.md similarity index 97% rename from faq/how_can_i_do_time-frequency_analysis_on_continuous_data.md rename to faq/tfr_continuous.md index da76332ba..956ef1ced 100644 --- a/faq/how_can_i_do_time-frequency_analysis_on_continuous_data.md +++ b/faq/tfr_continuous.md @@ -2,6 +2,8 @@ title: How can I do time-frequency analysis on continuous data? category: faq tags: [continuous, freq] +redirect_from: + - /faq/how_can_i_do_time-frequency_analysis_on_continuous_data/ --- # How can I do time-frequency analysis on continuous data? diff --git a/faq/why_does_my_tfr_contain_nans.md b/faq/tfr_nans.md similarity index 96% rename from faq/why_does_my_tfr_contain_nans.md rename to faq/tfr_nans.md index ec7939f28..1dced9596 100644 --- a/faq/why_does_my_tfr_contain_nans.md +++ b/faq/tfr_nans.md @@ -2,6 +2,8 @@ title: Why does my TFR contain NaNs? category: faq tags: [freq] +redirect_from: + - /faq/why_does_my_tfr_contain_nans/ --- # Why does my TFR contain NaNs? diff --git a/faq/why_does_my_tfr_look_strange.md b/faq/tfr_strangedemean.md similarity index 88% rename from faq/why_does_my_tfr_look_strange.md rename to faq/tfr_strangedemean.md index cee4cc59d..4d9da48cf 100644 --- a/faq/why_does_my_tfr_look_strange.md +++ b/faq/tfr_strangedemean.md @@ -2,13 +2,15 @@ title: Why does my TFR look strange (part I, demeaning)? category: faq tags: [mtmconvol, freq, preprocessing, artifact] +redirect_from: + - /faq/why_does_my_tfr_look_strange/ --- # Why does my TFR look strange (part I, demeaning)? If you use 'mtmconvol' as a method for frequency analysis it could happen that the Time-Frequency Representation of your data looks like this: -{% include image src="/assets/img/faq/why_does_my_tfr_look_strange/strangetfr1.png" width="400" %} +{% include image src="/assets/img/faq/tfr_strangedemean/strangetfr1.png" width="400" %} This phenomenon is caused by the time domain data having a non-zero DC component. This component leaks into the estimates of all time-frequency points in a variable (but patterned) way. The reason why this actually happens is related to the exact algorithm with which the TFR is computed in ft_freqanalysis_mtmconvol. The algorithm takes (computational) advantage of the fact that convolution in the time domain is mathematically equivalent to multiplication in the frequency domain. To this end, a fast fourier transform is applied to the time domain data, and it is combined with the fourier transform of the tapered basis functions. Importantly, no taper is applied to the data prior to fourier transformation. This leads to spectral leakage of the DC component across the whole frequency range. @@ -46,9 +48,9 @@ The following code shows the effect of a non-zero DC component on the TFR: ## Figure: TFR of chan02 with large DC component (left) and chan01 without DC component (right) after ft_freqanalysis without demeaning -{% include image src="/assets/img/faq/why_does_my_tfr_look_strange/strangetfr1.png" width="400" %} -{% include image src="/assets/img/faq/why_does_my_tfr_look_strange/strangetfr2.png" width="400" %} +{% include image src="/assets/img/faq/tfr_strangedemean/strangetfr1.png" width="400" %} +{% include image src="/assets/img/faq/tfr_strangedemean/strangetfr2.png" width="400" %} ## cfg.polyremoval -**Note,** in the above code `cfg.polyremoval = -1`. This option has been introduced in July 2011 (see [this email thread](http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004666.html)). The default behavior is `cfg.polyremoval = 0`, which means that the zero-order polynomial is removed, which is equal to demeaning. So if you're just using the default in ft_freqanalysis, your data will be automatically demeaned (you don't have to do in separately in ft_preprocessing), aiming to avoid these surprising effects. A value of -1 is NOT the default behavior, because it will lead to no demeaning whatsoever, and therefore shows the strange behavior. Also see [Why does my TFR look strange (part II)?](/faq/why_does_my_tfr_look_strange_part_ii) for info on detrending (is first-order polynomial removal). +**Note,** in the above code `cfg.polyremoval = -1`. This option has been introduced in July 2011 (see [this email thread](http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004666.html)). The default behavior is `cfg.polyremoval = 0`, which means that the zero-order polynomial is removed, which is equal to demeaning. So if you're just using the default in ft_freqanalysis, your data will be automatically demeaned (you don't have to do in separately in ft_preprocessing), aiming to avoid these surprising effects. A value of -1 is NOT the default behavior, because it will lead to no demeaning whatsoever, and therefore shows the strange behavior. Also see [Why does my TFR look strange (part II)?](/faq/tfr_strangedetrend) for info on detrending (is first-order polynomial removal). diff --git a/faq/why_does_my_tfr_look_strange_part_ii.md b/faq/tfr_strangedetrend.md similarity index 88% rename from faq/why_does_my_tfr_look_strange_part_ii.md rename to faq/tfr_strangedetrend.md index 03a754610..907429392 100644 --- a/faq/why_does_my_tfr_look_strange_part_ii.md +++ b/faq/tfr_strangedetrend.md @@ -2,13 +2,15 @@ title: Why does my TFR look strange (part II, detrending)? category: faq tags: [mtmconvol, freq, preprocessing, artifact, filter] +redirect_from: + - /faq/why_does_my_tfr_look_strange_part_ii/ --- # Why does my TFR look strange (part II, detrending)? If you use 'mtmconvol' as a method for frequency analysis it could happen that the Time-Frequency Representation of your data looks like this: -{% include image src="/assets/img/faq/why_does_my_tfr_look_strange_part_ii/strangetfr3.png" width="400" %} +{% include image src="/assets/img/faq/tfr_strangedetrend/strangetfr3.png" width="400" %} This phenomenon is caused by the time domain data having a slow low-frequency drift. This low-frequency component leaks into the estimates of all time-frequency points in a variable (but patterned) way. The reason why this actually happens is related to the fact that none of the tapered basis functions (i.e. windowed sine and cosine waves of increasing frequency) are exactly orthogonal to this slow drift. @@ -46,11 +48,11 @@ The following code shows the effect of a large amplitude low-frequency drift on ## Figure: Example data with a large amplitude low-frequency drift (1st) and its TFR (2nd) -{% include image src="/assets/img/faq/why_does_my_tfr_look_strange_part_ii/strangetfr4.png" width="300" %} -{% include image src="/assets/img/faq/why_does_my_tfr_look_strange_part_ii/strangetfr3.png" width="300" %} +{% include image src="/assets/img/faq/tfr_strangedetrend/strangetfr4.png" width="300" %} +{% include image src="/assets/img/faq/tfr_strangedetrend/strangetfr3.png" width="300" %} ## cfg.polyremoval -**Note,** in the above code `cfg.polyremoval = -1`. This option has been introduced in July 2011 (see [this email thread](http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004666.html)). The default behavior is cfg.polyremoval = 0, which means that the zero-order polynomial is removed, which is equal to demeaning. So if you're just using the default in ft_freqanalysis, your data will NOT be automatically detrended, thus you do have to specify `cfg.detrend = 'yes'` separately in ft_preprocessing to avoid these surprising effects. Alternatively, you can call ft_freqanalysis with `cfg.polyremoval = 1`, which removes BOTH the zero-order (demeaning) and first-order (detrending) polynomial. Also see [Why does my TFR look strange (part I, demeaning)?](/faq/why_does_my_tfr_look_strange). +**Note,** in the above code `cfg.polyremoval = -1`. This option has been introduced in July 2011 (see [this email thread](http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004666.html)). The default behavior is cfg.polyremoval = 0, which means that the zero-order polynomial is removed, which is equal to demeaning. So if you're just using the default in ft_freqanalysis, your data will NOT be automatically detrended, thus you do have to specify `cfg.detrend = 'yes'` separately in ft_preprocessing to avoid these surprising effects. Alternatively, you can call ft_freqanalysis with `cfg.polyremoval = 1`, which removes BOTH the zero-order (demeaning) and first-order (detrending) polynomial. Also see [Why does my TFR look strange (part I, demeaning)?](/faq/tfr_strangedemean). FYI, you can also specify a higher value (removing higher order polynomials), a value of 0 (only removing the mean), or -1 (no removal at all). diff --git a/faq/can_i_prevent_external_toolboxes_from_being_added_to_my_matlab_path.md b/faq/toolboxes_legacyvsexternal.md similarity index 94% rename from faq/can_i_prevent_external_toolboxes_from_being_added_to_my_matlab_path.md rename to faq/toolboxes_legacyvsexternal.md index 8d72932a8..d99cfc961 100644 --- a/faq/can_i_prevent_external_toolboxes_from_being_added_to_my_matlab_path.md +++ b/faq/toolboxes_legacyvsexternal.md @@ -2,6 +2,8 @@ title: Can I prevent "external" toolboxes from being added to my MATLAB path? category: faq tags: [matlab, toolbox, path] +redirect_from: + - /faq/can_i_prevent_external_toolboxes_from_being_added_to_my_matlab_path/ --- # Can I prevent "external" toolboxes from being added to my MATLAB path? diff --git a/faq/how_can_i_keep_track_of_the_changes_to_the_code.md b/faq/trackchanges.md similarity index 92% rename from faq/how_can_i_keep_track_of_the_changes_to_the_code.md rename to faq/trackchanges.md index f30b1564b..ec9294705 100644 --- a/faq/how_can_i_keep_track_of_the_changes_to_the_code.md +++ b/faq/trackchanges.md @@ -2,6 +2,8 @@ title: How can I keep track of changes to the code? category: faq tags: [download, development, cvs, svn, git] +redirect_from: + - /faq/how_can_i_keep_track_of_the_changes_to_the_code/ --- # How can I keep track of changes to the code? diff --git a/faq/how_can_i_transform_trigger_values_from_bits_to_decimal_representation_with_a_trialfun.md b/faq/trialfun_bit2decimal.md similarity index 96% rename from faq/how_can_i_transform_trigger_values_from_bits_to_decimal_representation_with_a_trialfun.md rename to faq/trialfun_bit2decimal.md index 3128072ba..e90523efb 100644 --- a/faq/how_can_i_transform_trigger_values_from_bits_to_decimal_representation_with_a_trialfun.md +++ b/faq/trialfun_bit2decimal.md @@ -2,6 +2,8 @@ title: How can I transform trigger values from bits to decimal representation with a trialfun? category: faq tags: [trialfun] +redirect_from: + - /faq/how_can_i_transform_trigger_values_from_bits_to_decimal_representation_with_a_trialfun/ --- # How can I transform trigger values from bits to decimal representation with a trialfun? diff --git a/faq/is_it_possible_to_keep_track_of_trial-specific_information_in_my_fieldtrip_analysis_pipeline.md b/faq/trialinfo.md similarity index 95% rename from faq/is_it_possible_to_keep_track_of_trial-specific_information_in_my_fieldtrip_analysis_pipeline.md rename to faq/trialinfo.md index 8c2a0f0b5..15b3b7190 100644 --- a/faq/is_it_possible_to_keep_track_of_trial-specific_information_in_my_fieldtrip_analysis_pipeline.md +++ b/faq/trialinfo.md @@ -2,6 +2,8 @@ title: Is it possible to keep track of trial-specific information in my analysis pipeline? category: faq tags: [trialinfo, trialdef, trialfun] +redirect_from: + - /faq/is_it_possible_to_keep_track_of_trial-specific_information_in_my_fieldtrip_analysis_pipeline/ --- # Is it possible to keep track of trial-specific information in my analysis pipeline? diff --git a/faq/i_used_to_work_with_trl-matrices_that_have_more_than_3_columns._why_is_this_not_supported_anymore.md b/faq/trialinfo_trl.md similarity index 94% rename from faq/i_used_to_work_with_trl-matrices_that_have_more_than_3_columns._why_is_this_not_supported_anymore.md rename to faq/trialinfo_trl.md index fa7beddcb..266d6e012 100644 --- a/faq/i_used_to_work_with_trl-matrices_that_have_more_than_3_columns._why_is_this_not_supported_anymore.md +++ b/faq/trialinfo_trl.md @@ -2,6 +2,8 @@ title: I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore? category: faq tags: [trialinfo, trialdef, trialfun] +redirect_from: + - /faq/i_used_to_work_with_trl-matrices_that_have_more_than_3_columns._why_is_this_not_supported_anymore/ --- # I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore? diff --git a/faq/video.md b/faq/video.md index f8876ed8a..53ac3a4fa 100644 --- a/faq/video.md +++ b/faq/video.md @@ -11,5 +11,3 @@ Yes and no. Some material is online available, but not all. Please see the [vide We are planning to record more future lectures on camera. However, that does not automatically mean that all recorded material will automatically be posted online. Ideally we would indeed post it on our youTube channel, but making (i.e. shooting and editing) good quality videos is not easy and making bad quality videos available would not be beneficial for the project in the long run. Also, not all presenters feel comfortable with having their presentation in the public. So it is part of our ongoing efforts to improve the dissemination of FieldTrip and the methods implemented in it, and we do hope that we will get the hang of making it available as [MOOC](https://en.wikipedia.org/wiki/Massive_open_online_course). - -In case you want to know more about how we perform the recordings, please have a look [here](/development/guideline/video). diff --git a/faq/why_largest_peak_spectrum.md b/faq/why_largest_peak_spectrum.md index 9359eea75..3d3399233 100644 --- a/faq/why_largest_peak_spectrum.md +++ b/faq/why_largest_peak_spectrum.md @@ -2,6 +2,8 @@ title: Why is the largest peak in the spectrum at the frequency which is 1/segment length? category: faq tags: [mtmfft, freq, demean] +redirect_from: + - /faq/why_largest_peak_spectrum/ --- # Why is the largest peak in the spectrum at the frequency which is 1/segment length? diff --git a/faq/can_i_organize_my_own_workshop.md b/faq/workshop.md similarity index 93% rename from faq/can_i_organize_my_own_workshop.md rename to faq/workshop.md index b57ce1c8e..0ad790332 100644 --- a/faq/can_i_organize_my_own_workshop.md +++ b/faq/workshop.md @@ -2,6 +2,8 @@ title: Can I organize my own FieldTrip workshop? category: faq tags: [workshop] +redirect_from: + - /faq/can_i_organize_my_own_workshop/ --- # Can I organize my own FieldTrip workshop? diff --git a/faq/how_should_i_prepare_for_the_upcoming_fieldtrip_workshop.md b/faq/workshop_preparation.md similarity index 96% rename from faq/how_should_i_prepare_for_the_upcoming_fieldtrip_workshop.md rename to faq/workshop_preparation.md index 3e9cb0a4f..d4c207d9e 100644 --- a/faq/how_should_i_prepare_for_the_upcoming_fieldtrip_workshop.md +++ b/faq/workshop_preparation.md @@ -2,6 +2,8 @@ title: How should I prepare for the upcoming FieldTrip workshop? category: faq tags: [workshop] +redirect_from: + - /faq/how_should_i_prepare_for_the_upcoming_fieldtrip_workshop/ --- # How should I prepare for the upcoming FieldTrip workshop? diff --git a/faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format.md b/faq/writedata_matbin.md similarity index 97% rename from faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format.md rename to faq/writedata_matbin.md index 3d8ee0cdf..e92d45749 100644 --- a/faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format.md +++ b/faq/writedata_matbin.md @@ -2,6 +2,8 @@ title: Reading is slow, can I write my raw data to a more efficient file format? category: faq tags: [preprocessing, dataformat, raw] +redirect_from: + - /faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format/ --- # Reading is slow, can I write my raw data to a more efficient file format? diff --git a/template/layout.md b/template/layout.md index 57ef83715..0f94b86ca 100644 --- a/template/layout.md +++ b/template/layout.md @@ -48,10 +48,10 @@ This is a custom 64-channel arrangement for the Max Planck Institute for Psychol ##### acticap-64ch-standard2.mat -This is the standard 64-channel actiCAP arrangement from [Brain Products](http://www.brainproducts.com/files/public/downloads/actiCAP-64-channel-Standard-2_1201.pdf). It is based on the same coordinates as the EasyCap electrode caps. This particular layout was created using the [easycapM1 layout](/assets/img/template/layout/easycapm1.png) and then removing eight electrodes (FPz, Iz, F9, F10, P9, P10, O9, O10) which are not present in the cap. Furthermore, two electrodes (AFz, FCz) were renamed to their purpose of being Ground (Gnd) and Reference (Ref) electrode. +This is the standard 64-channel actiCAP arrangement from [Brain Products](http://www.brainproducts.com/files/public/downloads/actiCAP-64-channel-Standard-2_1201.pdf). It is based on the same coordinates as the EasyCap electrode caps. This particular layout was created from the EasyCap M1 layout and then removing eight electrodes (FPz, Iz, F9, F10, P9, P10, O9, O10) which are not present in this cap. Furthermore, two electrodes (AFz, FCz) were renamed to their purpose of being Ground (Gnd) and Reference (Ref) electrode. {% include image src="/assets/img/template/layout/original/acticap-64-channel-standard-2.jpg" width="200" %} -{% include image src="/assets/img/template/layout/acticap-64-channel-standard-2.mat.jpg" width="200" %} +{% include image src="/assets/img/template/layout/acticap-64ch-standard2.mat.png" width="200" %} ##### BrainProducts R-Net diff --git a/tutorial/eeg_language.md b/tutorial/eeg_language.md index 50b6d5006..a735756ff 100644 --- a/tutorial/eeg_language.md +++ b/tutorial/eeg_language.md @@ -23,7 +23,7 @@ The data also contains response events for the subjects' responses to the task c _Figure 1. Experimental stimuli and conditions_ -Continuous EEG was registered using a 64 channel ActiCap system (Brain Products GmbH) filtered at 0.2–200 Hz and sampled at 500 Hz with the BrainVision Recorder Professional software (Brain Products GmbH). An [equidistant electrode cap](/assets/img/template/layout/easycapm10.png) was used to position 60 electrodes on the scalp as follows: +Continuous EEG was registered using a 64 channel ActiCap system (Brain Products GmbH) filtered at 0.2–200 Hz and sampled at 500 Hz with the BrainVision Recorder Professional software (Brain Products GmbH). An [M10 equidistant electrode cap](/assets/img/template/layout/easycapm10.mat.png) was used to position 60 electrodes on the scalp as follows: {% include image src="/assets/img/workshop/madrid2019/datasets/simanova_fig2.png" width="400" %} diff --git a/tutorial/human_ecog.md b/tutorial/human_ecog.md index c021ea215..b199110c3 100644 --- a/tutorial/human_ecog.md +++ b/tutorial/human_ecog.md @@ -471,7 +471,7 @@ CRITICAL STEP Identifying bad channels is important for avoiding the contaminati ### Interactive plotting -**47**) For an anatomically informed exploration of the multidimensional outcome of an analysis, create a layout based on the three-dimensional electrode locations. This layout is a symbolic representation in which the channels are projected on the two-dimensional medium offered by paper or a computer screen, see also the [layout tutorial](tutorial/layout). +**47**) For an anatomically informed exploration of the multidimensional outcome of an analysis, create a layout based on the three-dimensional electrode locations. This layout is a symbolic representation in which the channels are projected on the two-dimensional medium offered by paper or a computer screen, see also the [layout tutorial](/tutorial/layout). The layout is complemented by an automatic outline of the cortical sheet that is specified in cfg.headshape. The cfg.boxchannel option allows selecting channels whose two-dimensional distances are used to determine the plotting box sizes in the following step. diff --git a/tutorial/salzburg.md b/tutorial/salzburg.md index 7f98d83b3..2c1355f23 100644 --- a/tutorial/salzburg.md +++ b/tutorial/salzburg.md @@ -348,7 +348,7 @@ For this step the individual volume is required, which can be downloaded [here]( ### Compute the leadfield -We first create the leadfield using [**reference: ft_prepare_leadfield](/\*\*reference/ ft_prepare_leadfield) using the individual head model from the previous step, the sensor array and the sourcemodel. +We first create the leadfield using **[ft_prepare_leadfield](/reference/ft_prepare_leadfield)** using the individual head model from the previous step, the sensor array and the sourcemodel. cfg = []; cfg.channel = dataica.label; % ensure that rejected sensors are not present @@ -358,7 +358,7 @@ We first create the leadfield using [**reference: ft_prepare_leadfield](/\*\*ref cfg.grid = sourcemodel; [grid] = ft_prepare_leadfield(cfg); -We want to reconstruct the locations of the M100 component. In the present case this component is maximal around 50 to 180ms post stimulus onset. Therefore we segment the data around this interval using [**reference: ft_redefinetrial](/\*\*reference/ ft_redefinetrial). Furthermore we would contrast the source solution against a prestimulus baseline of equal length. +We want to reconstruct the locations of the M100 component. In the present case this component is maximal around 50 to 180ms post stimulus onset. Therefore we segment the data around this interval using **[ft_redefinetrial](/reference/ft_redefinetrial)**. Furthermore we would contrast the source solution against a prestimulus baseline of equal length. cfg = []; cfg.toilim = [-.18 -.05]; @@ -368,7 +368,7 @@ We want to reconstruct the locations of the M100 component. In the present case ### Compute data covariance -The spatial filters are computed on the basis of the covariance matrix obtained from the data. In the following step we compute this matrix for an interval accounting for the pre and post stimulus intervals of interest. For this we make a call to [**reference: ft_timelockanalysis](/**reference/ ft_timelockanalysis) with the ** cfg.covariance = 'yes';** and ** cfg.covariancewindow = [xx yy];\*\*. These configuration will ensure the covariance matrix to be present in the output structure. +The spatial filters are computed on the basis of the covariance matrix obtained from the data. In the following step we compute this matrix for an interval accounting for the pre and post stimulus intervals of interest. For this we make a call to **[ft_timelockanalysis](/reference/ ft_timelockanalysis)** with `cfg.covariance = 'yes'` and `cfg.covariancewindow = [xx yy]`. These configuration options will ensure the covariance matrix to be present in the output structure. cfg = []; cfg.covariance='yes'; @@ -380,7 +380,7 @@ The spatial filters are computed on the basis of the covariance matrix obtained avgpre = ft_timelockanalysis(cfg,datapre); avgpst = ft_timelockanalysis(cfg,datapost); -Now we make a first call to [** reference: ft_sourceanalysis](/\*\* reference/ ft_sourceanalysis) in order to compute the spatial filters on the basis of the entire data and keep them in the output for a later use. +Now we make a first call to **[ft_sourceanalysis](/reference/ft_sourceanalysis)** in order to compute the spatial filters on the basis of the entire data and keep them in the output for a later use. cfg=[]; cfg.method='lcmv'; @@ -409,7 +409,7 @@ Now we can subtract the two conditions, normalize by the power in the pre stimul cfg.operation = '((x1-x2)./x2)*100'; S1bl=ft_math(cfg,sourcepstS1,sourcepreS1); -The result is then interpolated on the template mri after the individual dipole locations are set back to be equal with the template_grid locations. This is done with [**reference: ft_sourceinterpolate](/\*\*reference/ ft_sourceinterpolate). +The result is then interpolated on the template mri after the individual dipole locations are set back to be equal with the template_grid locations. This is done with **[ft_sourceinterpolate](/reference/ft_sourceinterpolate)**. if isunix templatefile = '~fieldtrip/template/anatomy/single_subj_T1.nii'; @@ -424,7 +424,7 @@ The result is then interpolated on the template mri after the individual dipole cfg.interpmethod = 'nearest'; source_int = ft_sourceinterpolate(cfg, S1bl, template_mri); -Finally, we can plot the result using [**reference: ft_sourceplot](/\*\*reference/ ft_sourceplot). +Finally, we can plot the result using **[ft_sourceplot](/reference/ft_sourceplot)**. cfg = []; cfg.method = 'ortho'; @@ -437,7 +437,7 @@ Finally, we can plot the result using [**reference: ft_sourceplot](/\*\*referenc ### Plot the result in parceled brain space -It is now possible to integrate the result over the brain parcels using the brain atlas and [**reference: ft_sourceparcellate](/**reference/ ft_sourceparcellate). First, we load the template mri corresponding to the brain atlas located in the spm8/templates directory and interpolate the result on this template once more. Subsequently we call [**reference: ft_sourceparcellate](/\*\*reference/ ft_sourceparcellate) with this sourceinterpolated structure and the brain atlas. +It is now possible to integrate the result over the brain parcels using the brain atlas and **[ft_sourceparcellate](/reference/ft_sourceparcellate)**. First, we load the template mri corresponding to the brain atlas located in the spm8/templates directory and interpolate the result on this template once more. Subsequently we call **[ft_sourceparcellate](/reference/ft_sourceparcellate)** with this sourceinterpolated structure and the brain atlas. templatefile = '~fieldtrip/external/spm8/templates/T1.nii'; template_mri = ft_read_mri(templatefile); @@ -618,7 +618,7 @@ We repeat the steps from above and plot the result in parceled brain space. {% include image src="/assets/img/tutorial/salzburg/figure12.png" %} -The two different thresholds (80% of maximum vs. permutation statistics) seem to convey slightly different results. While a predominant activation in the left heschl gyrus was observed as a maximal difference between pre and post stimulus interval, the statistical evaluation suggest right temporal activation together with distributed activity in prefrontal areas. At first this appears somewhat puzzling yet evaluating the spatial extend of the activity in the left heschl gyrus suggest a very focal circumscribed source likely involving very few voxels. On the other hand during the call to [**reference: ft_sourcestatistics](/\*\*reference/ ft_sourcestatistics) we used a particular configuration for the clusterstatistics- 'maxsum'. Using this option only voxel clusters with largest summed activity are considered during the sampling of the distribution. The right temporal area is characterized by rather broad spatial homogeneity that leads to greater statistical sensitivity. Instead of 'maxsum' it is also possible to use 'max' values during the montercarlo sampling of the distribution. When we do so it becomes apparent that on the basis of the activity in the left heschl gyrus we can reject H0 too. +The two different thresholds (80% of maximum vs. permutation statistics) seem to convey slightly different results. While a predominant activation in the left heschl gyrus was observed as a maximal difference between pre and post stimulus interval, the statistical evaluation suggest right temporal activation together with distributed activity in prefrontal areas. At first this appears somewhat puzzling yet evaluating the spatial extend of the activity in the left heschl gyrus suggest a very focal circumscribed source likely involving very few voxels. On the other hand during the call to **[ft_sourcestatistics](/reference/ft_sourcestatistics)** we used a particular configuration for the clusterstatistics- 'maxsum'. Using this option only voxel clusters with largest summed activity are considered during the sampling of the distribution. The right temporal area is characterized by rather broad spatial homogeneity that leads to greater statistical sensitivity. Instead of 'maxsum' it is also possible to use 'max' values during the montercarlo sampling of the distribution. When we do so it becomes apparent that on the basis of the activity in the left heschl gyrus we can reject H0 too. {% include image src="/assets/img/tutorial/salzburg/figure13.png" width="800" %} @@ -761,7 +761,7 @@ Now we compute the source wave forms, plot and evaluate the result. One of various and equally valid methods of assessing connectivity is the concept of coherence. By using this metric we want to evaluate the presence of a temporal relationship between the nodes as a function of frequency. This can be done for the entire time interval of interest or by applying sliding window approach and represent the result as function of time and frequency. The latter is applied below. -First, we use **[ft_freqanalysis](/reference/ft_freqanalysis)** much in the same way as demonstrated above. The only difference is that the phase information is kept in the output by the configuration option **cfg.output = 'powandcsd'**. +First, we use **[ft_freqanalysis](/reference/ft_freqanalysis)** much in the same way as demonstrated above. The only difference is that the phase information is kept in the output by the configuration option `cfg.output = 'powandcsd'`. cfg = []; cfg.method = 'mtmconvol'; @@ -789,6 +789,7 @@ Now we can plot and evaluate the result of the power estimates essentially confi {% include image src="/assets/img/tutorial/salzburg/figure15.png" width="600" %} The slow frequency increases in energy are likely related to the evoked components in the data. In addition an increase in amplitude around 10-14Hz is also observed. In the next step we would like to evaluate to what extend this patterns represent a temporal relationship between the nodes. + First we compute coherence using **[ft_connectivityanalysis](/reference/ft_connectivityanalysis)**. cfg = []; @@ -928,5 +929,3 @@ Now we plot the results of the original and the flipped version of the same data figure; ft_connectivityplot(cfg,granger,grangerflip); {% include image src="/assets/img/tutorial/salzburg/figure19.png" %} - -## Summary and conclusion diff --git a/workshop/cuttingeegx/squids_vs_opms.md b/workshop/cuttingeegx/squids_vs_opms.md index b06ae97e1..1dc37cbc4 100644 --- a/workshop/cuttingeegx/squids_vs_opms.md +++ b/workshop/cuttingeegx/squids_vs_opms.md @@ -20,7 +20,7 @@ OPMs are magnetometers, as their name suggests. Magnetometers are more sensitive Unlike SQUID systems, which have standard coregistration strategies, OPMs don't have a single coregistration standard. In this tutorial, we coregister the OPMs with the MRI using an optical 3D scanner which captures the participant’s facial features along with the OPM helmet ([Zetter et al., 2019](https://www.nature.com/articles/s41598-019-41763-4)). -This tutorial combines the FieldTrip tutorials on [preprocessing of Optically Pumped Magnetometer (OPM) data](tutorial/preprocessing_opm/) and [coregistration of Optically Pumped Magnetometer (OPM) data](tutorial/coregistration_opm/). It does not cover follow-up analyses (like source reconstruction) which in principle should not differ from the SQUID follow-up analyses, or alternative coregistration methods which are covered in the tutorial on [coregistration of Optically Pumped Magnetometer (OPM) data](tutorial/coregistration_opm/). +This tutorial combines the FieldTrip tutorials on [preprocessing of Optically Pumped Magnetometer (OPM) data](/tutorial/preprocessing_opm/) and [coregistration of Optically Pumped Magnetometer (OPM) data](/tutorial/coregistration_opm/). It does not cover follow-up analyses (like source reconstruction) which in principle should not differ from the SQUID follow-up analyses, or alternative coregistration methods which are covered in the tutorial on [coregistration of Optically Pumped Magnetometer (OPM) data](/tutorial/coregistration_opm/). ## Background @@ -382,7 +382,7 @@ save shape shape To understand coregistration, you first need to know what [coordinate systems](/faq/coordsys) are. Coregistration is about aligning data that is initially expressed in different coordinate systems into a single coordinate system. -Start by plotting the MRI, SQUID sensors, and Polhemus headshape to see in which coordinate systems these are expressed. You can use **[ft_determine_coordsys](/utilities/ft_determine_coordsys)** for that. +Start by plotting the MRI, SQUID sensors, and Polhemus headshape to see in which coordinate systems these are expressed. You can use **[ft_determine_coordsys](/reference/utilities/ft_determine_coordsys)** for that. {% include markup/end %} diff --git a/workshop/madrid2019/tutorial_freq.md b/workshop/madrid2019/tutorial_freq.md index 34c7ac017..9d322ac0c 100644 --- a/workshop/madrid2019/tutorial_freq.md +++ b/workshop/madrid2019/tutorial_freq.md @@ -39,7 +39,7 @@ at each frequency, and multiplying that with a Gaussian taper. The width of the Gaussian taper is scaled with the frequency, such that there are always a fixed number of cycles in the wavelet, for example 3 or 5. -{% include image src="/assets/img/tutorial/timefrequencyanalysis/tfrtiles.png" width="600" %} +{% include image src="/assets/img/workshop/madrid2019/tutorial_freq/tfrtiles.png" width="600" %} _Figure: Time and frequency smoothing. (a) For a fixed length time window the time and frequency smoothing remains fixed. (b) For time windows that @@ -63,7 +63,7 @@ perform the following steps: - Compute the power spectra using **[ft_freqanalysis](/reference/ft_freqanalysis)** - Visualize the results for all channels and for selected channels. You can make time-frequency plots using **[ft_singleplotTFR](/reference/ft_singleplotTFR)**, **[ft_multiplotTFR](/reference/ft_multiplotTFR)** and **[ft_topoplotTFR](/reference/ft_topoplotTFR)**. For power spectra without time dimension, you can use **[ft_singleplotER](/reference/ft_singleplotER)**, **[ft_multiplotER](/reference/ft_multiplotER)** and **[ft_topoplotER](/reference/ft_topoplotER)**. -{% include image src="/assets/img/tutorial/timefrequencyanalysis/tfr_pipelinenew.png" width="200" %} +{% include image src="/assets/img/workshop/madrid2019/tutorial_freq/tfr_pipelinenew.png" width="200" %} _Figure: Schematic overview of the steps in time-frequency analysis_ diff --git a/workshop/oxford2019/sensor_analysis_plusminus.md b/workshop/oxford2019/sensor_analysis_plusminus.md index 83c6cdadc..af1a900eb 100644 --- a/workshop/oxford2019/sensor_analysis_plusminus.md +++ b/workshop/oxford2019/sensor_analysis_plusminus.md @@ -13,7 +13,7 @@ This tutorial was written specifically for the workshop in Oxford in May 2019, a In this tutorial, we will provide an overview of several sensor-level analyses to help you get started working with FieldTrip. We will work on a dataset (Schoffelen, Poort, Oostenveld, & Fries (2011) Selective Movement Preparation Is Subserved by Selective Increases in Corticomuscular Gamma-Band Coherence. J Neurosci. 31(18):6750-6758) collected during an experiment where subjects were instructed to fixate on a screen. Each trial started with the presentation of a cue pointing either rightward or leftward. This cue indicated which hand the subject had to use for the trial's response. Next, the subjects were instructed to extend both their wrists. After a baseline interval of 1s, an inward drifting grating was visually presented. Then, after an unpredictable delay, the stimulus changed speed, after which the subjects had to increase their wrist extension on the one cued side only. This experimental design is illustrated in Figure 1. Magneto-encephalography (MEG) data was collected using a 151-channel CTF system. Also, electromyography (EMG) data was collected from electrodes attached to the bilateral musculus extensor carpi radialis longus. -{% include image src="/assets/img/tutorial/sensor_analysis/design.png" %} +{% include image src="/assets/img/workshop/oxford2019/sensor_analysis_plusminus/design.png" %} _Figure 1: illustration of the experimental paradigm._ @@ -115,7 +115,7 @@ Time point 0 in all trials corresponds to the onset of the visual stimulation. T ylabel('trial number'); xlabel('time (s)'); -{% include image src="/assets/img/tutorial/sensor_analysis/multipletrials.png" %} +{% include image src="/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multipletrials.png" %} _Figure 1a: Some example trials, with time t=0 marked._ @@ -146,7 +146,7 @@ FieldTrip provides several options for visualizing the results of event-related Note that we request channel labels and head outline showing, and with a particular template layout corresponding to our MEG acquisition system. The output should look like this: -{% include image src="/assets/img/tutorial/sensor_analysis/multiploter.png" %} +{% include image src="/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiploter.png" %} _Figure 2: event-related field for each MEG sensor._ @@ -154,19 +154,19 @@ As you can see, the event-related field for each MEG sensor is displayed at a lo The nice thing about this multiplot is that it is interactive: it is possible to select sensors and view an average plot (corresponding to an **[ft_singleplotER](/reference/ft_singleplotER)**) of those sensors. There seems to be an interesting deflection in the ERF around the left occipitoparietal sensors. Go ahead and select those, and click the selection box that comes up. -{% include image src="/assets/img/tutorial/sensor_analysis/multiploter_interactive.png" %} +{% include image src="/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiploter_interactive.png" %} _Figure 3: click the box to show the average of the selected sensors._ The plot that comes up shows a major deflection around 300m -{% include image src="/assets/img/tutorial/sensor_analysis/singleploter.png" %} +{% include image src="/assets/img/workshop/oxford2019/sensor_analysis_plusminus/singleploter.png" %} _Figure 4: average ERF for some left posterior sensors._ Again, you can select a time range and click it to bring up a topographical plot (**[ft_topoplotER](/reference/ft_topoplotER)**) of the ERF averaged over the selected time window. Select the peak around 300ms and click it. -{% include image src="/assets/img/tutorial/sensor_analysis/topoploter.png" %} +{% include image src="/assets/img/workshop/oxford2019/sensor_analysis_plusminus/topoploter.png" %} _Figure 5: topographical representation of the ERF deflection around 300ms after visual stimulus onset._ @@ -223,7 +223,7 @@ Oscillatory components contained in the ongoing EEG or MEG signal often show pow Calculating time-frequency representations of power is done using a sliding time window. This can be done according to two principles: either the time window has a fixed length independent of frequency, or the time window decreases in length with increased frequency. For each time window the power is calculated. Prior to calculating the power one or more tapers are multiplied with the data. The aim of the tapers is to reduce spectral leakage and control the frequency smoothing. -{% include image src="/assets/img/tutorial/sensor_analysis/tfrtiles.png" %} +{% include image src="/assets/img/workshop/oxford2019/sensor_analysis_plusminus/tfrtiles.png" %} _Figure 6: Time and frequency smoothing. (a) For a fixed length time window the time and frequency smoothing remains fixed. (b) For time windows that decrease with frequency, the temporal smoothing decreases and the frequency smoothing increases._ @@ -285,7 +285,7 @@ Then we can plot the results using **[ft_multiplotTFR](/reference/ft_multiplotTF Note the baseline and baselinetype parameters. These govern what baseline correction is applied to the data before plotting. In this case, we want to plot the relative change of our power data with respect to the interval between -0.8s and 0s (corresponding to the no-stimulation baseline interval in the experimental design). -{% include image src="/assets/img/tutorial/sensor_analysis/multiplottfr.png" %} +{% include image src="/assets/img/workshop/oxford2019/sensor_analysis_plusminus/multiplottfr.png" %} _Figure 7: Time-frequency representation using a Hanning taper with a fixed window length._ @@ -299,7 +299,7 @@ Click around the multiplot to explore the visual gamma response and its topograp In a next step, you can get an overview of your analyses by clicking on the FieldTrip menu item and selecting "Show pipeline": -{% include image src="/assets/img/tutorial/sensor_analysis/figurepipeline.png" %} +{% include image src="/assets/img/workshop/oxford2019/sensor_analysis_plusminus/figurepipeline.png" %} Exactly the same can be achieved using **[ft_analysispipeline](/reference/ft_analysispipeline)** as follow @@ -308,7 +308,7 @@ Exactly the same can be achieved using **[ft_analysispipeline](/reference/ft_ana The function ft_analysispipeline puts all conducted analysis steps into perspective and visualizes them in a flowchart: -{% include image src="/assets/img/tutorial/sensor_analysis/analysispipeline_sensor_analysis.png" %} +{% include image src="/assets/img/workshop/oxford2019/sensor_analysis_plusminus/analysispipeline_sensor_analysis.png" %} By clicking on one of the boxes (in MATLAB), a new figure will appear that shows all cfg-options that were used to in the respective function.