Rename folders (qsiprep --> qsirecon)

PennLINC · Aug 9, 2024 · 131b085 · 131b085
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diff --git a/qsiprep/__init__.py → qsirecon/__init__.py b/qsiprep/__init__.py → qsirecon/__init__.py
diff --git a/qsiprep/_warnings.py → qsirecon/_warnings.py b/qsiprep/_warnings.py → qsirecon/_warnings.py
diff --git a/qsiprep/cli/__init__.py → qsirecon/cli/__init__.py b/qsiprep/cli/__init__.py → qsirecon/cli/__init__.py
diff --git a/qsiprep/cli/convertODFs.py → qsirecon/cli/convertODFs.py b/qsiprep/cli/convertODFs.py → qsirecon/cli/convertODFs.py
diff --git a/qsiprep/cli/group_report.py → qsirecon/cli/group_report.py b/qsiprep/cli/group_report.py → qsirecon/cli/group_report.py
diff --git a/qsiprep/cli/parser.py → qsirecon/cli/parser.py b/qsiprep/cli/parser.py → qsirecon/cli/parser.py
diff --git a/qsiprep/cli/recon_plot.py → qsirecon/cli/recon_plot.py b/qsiprep/cli/recon_plot.py → qsirecon/cli/recon_plot.py
diff --git a/qsiprep/cli/run.py → qsirecon/cli/run.py b/qsiprep/cli/run.py → qsirecon/cli/run.py
diff --git a/qsiprep/cli/version.py → qsirecon/cli/version.py b/qsiprep/cli/version.py → qsirecon/cli/version.py
diff --git a/qsiprep/cli/workflow.py → qsirecon/cli/workflow.py b/qsiprep/cli/workflow.py → qsirecon/cli/workflow.py
diff --git a/qsiprep/config.py → qsirecon/config.py b/qsiprep/config.py → qsirecon/config.py
diff --git a/qsiprep/data/FreeSurfer2dseg.txt → qsirecon/data/FreeSurfer2dseg.txt b/qsiprep/data/FreeSurfer2dseg.txt → qsirecon/data/FreeSurfer2dseg.txt
diff --git a/qsiprep/data/FreeSurferColorLUT.txt → qsirecon/data/FreeSurferColorLUT.txt b/qsiprep/data/FreeSurferColorLUT.txt → qsirecon/data/FreeSurferColorLUT.txt
diff --git a/qsiprep/data/NOTICE → qsirecon/data/NOTICE b/qsiprep/data/NOTICE → qsirecon/data/NOTICE
diff --git a/qsiprep/data/__init__.py → qsirecon/data/__init__.py b/qsiprep/data/__init__.py → qsirecon/data/__init__.py
diff --git a/qsiprep/data/abcd/dataset_description.json → qsirecon/data/abcd/dataset_description.json b/qsiprep/data/abcd/dataset_description.json → qsirecon/data/abcd/dataset_description.json
diff --git a/...ta/abcd/sub-abcd/anat/sub-abcd_T1w.nii.gz → ...ta/abcd/sub-abcd/anat/sub-abcd_T1w.nii.gz b/...ta/abcd/sub-abcd/anat/sub-abcd_T1w.nii.gz → ...ta/abcd/sub-abcd/anat/sub-abcd_T1w.nii.gz
diff --git a/...data/abcd/sub-abcd/anat/sub-abcd_T2w.json → ...data/abcd/sub-abcd/anat/sub-abcd_T2w.json b/...data/abcd/sub-abcd/anat/sub-abcd_T2w.json → ...data/abcd/sub-abcd/anat/sub-abcd_T2w.json
diff --git a/...ta/abcd/sub-abcd/anat/sub-abcd_T2w.nii.gz → ...ta/abcd/sub-abcd/anat/sub-abcd_T2w.nii.gz b/...ta/abcd/sub-abcd/anat/sub-abcd_T2w.nii.gz → ...ta/abcd/sub-abcd/anat/sub-abcd_T2w.nii.gz
diff --git a/.../data/abcd/sub-abcd/dwi/sub-abcd_dwi.bval → .../data/abcd/sub-abcd/dwi/sub-abcd_dwi.bval b/.../data/abcd/sub-abcd/dwi/sub-abcd_dwi.bval → .../data/abcd/sub-abcd/dwi/sub-abcd_dwi.bval
diff --git a/.../data/abcd/sub-abcd/dwi/sub-abcd_dwi.bvec → .../data/abcd/sub-abcd/dwi/sub-abcd_dwi.bvec b/.../data/abcd/sub-abcd/dwi/sub-abcd_dwi.bvec → .../data/abcd/sub-abcd/dwi/sub-abcd_dwi.bvec
diff --git a/.../data/abcd/sub-abcd/dwi/sub-abcd_dwi.json → .../data/abcd/sub-abcd/dwi/sub-abcd_dwi.json b/.../data/abcd/sub-abcd/dwi/sub-abcd_dwi.json → .../data/abcd/sub-abcd/dwi/sub-abcd_dwi.json
diff --git a/...ata/abcd/sub-abcd/dwi/sub-abcd_dwi.nii.gz → ...ata/abcd/sub-abcd/dwi/sub-abcd_dwi.nii.gz b/...ata/abcd/sub-abcd/dwi/sub-abcd_dwi.nii.gz → ...ata/abcd/sub-abcd/dwi/sub-abcd_dwi.nii.gz
diff --git a/...cd/sub-abcd/fmap/sub-abcd_dir-AP_epi.json → ...cd/sub-abcd/fmap/sub-abcd_dir-AP_epi.json b/...cd/sub-abcd/fmap/sub-abcd_dir-AP_epi.json → ...cd/sub-abcd/fmap/sub-abcd_dir-AP_epi.json
diff --git a/.../sub-abcd/fmap/sub-abcd_dir-AP_epi.nii.gz → .../sub-abcd/fmap/sub-abcd_dir-AP_epi.nii.gz b/.../sub-abcd/fmap/sub-abcd_dir-AP_epi.nii.gz → .../sub-abcd/fmap/sub-abcd_dir-AP_epi.nii.gz
diff --git a/...cd/sub-abcd/fmap/sub-abcd_dir-PA_epi.json → ...cd/sub-abcd/fmap/sub-abcd_dir-PA_epi.json b/...cd/sub-abcd/fmap/sub-abcd_dir-PA_epi.json → ...cd/sub-abcd/fmap/sub-abcd_dir-PA_epi.json
diff --git a/.../sub-abcd/fmap/sub-abcd_dir-PA_epi.nii.gz → .../sub-abcd/fmap/sub-abcd_dir-PA_epi.nii.gz b/.../sub-abcd/fmap/sub-abcd_dir-PA_epi.nii.gz → .../sub-abcd/fmap/sub-abcd_dir-PA_epi.nii.gz
diff --git a/qsiprep/data/affine.json → qsirecon/data/affine.json b/qsiprep/data/affine.json → qsirecon/data/affine.json
diff --git a/qsiprep/data/b02b0_1.cnf → qsirecon/data/b02b0_1.cnf b/qsiprep/data/b02b0_1.cnf → qsirecon/data/b02b0_1.cnf
diff --git a/qsiprep/data/bids.json → qsirecon/data/bids.json b/qsiprep/data/bids.json → qsirecon/data/bids.json
diff --git a/qsiprep/data/boilerplate.bib → qsirecon/data/boilerplate.bib b/qsiprep/data/boilerplate.bib → qsirecon/data/boilerplate.bib
diff --git a/qsiprep/data/buds/sub-1/anat/sub-1_T1w.json → qsirecon/data/buds/sub-1/anat/sub-1_T1w.json b/qsiprep/data/buds/sub-1/anat/sub-1_T1w.json → qsirecon/data/buds/sub-1/anat/sub-1_T1w.json
diff --git a/...rep/data/buds/sub-1/anat/sub-1_T1w.nii.gz → ...con/data/buds/sub-1/anat/sub-1_T1w.nii.gz b/...rep/data/buds/sub-1/anat/sub-1_T1w.nii.gz → ...con/data/buds/sub-1/anat/sub-1_T1w.nii.gz
diff --git a/...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.bval → ...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.bval b/...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.bval → ...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.bval
diff --git a/...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.bvec → ...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.bvec b/...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.bvec → ...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.bvec
diff --git a/...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.json → ...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.json b/...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.json → ...data/buds/sub-1/dwi/sub-1_dir-j-_dwi.json
diff --git a/...ta/buds/sub-1/dwi/sub-1_dir-j-_dwi.nii.gz → ...ta/buds/sub-1/dwi/sub-1_dir-j-_dwi.nii.gz b/...ta/buds/sub-1/dwi/sub-1_dir-j-_dwi.nii.gz → ...ta/buds/sub-1/dwi/sub-1_dir-j-_dwi.nii.gz
diff --git a/.../data/buds/sub-1/dwi/sub-1_dir-j_dwi.bval → .../data/buds/sub-1/dwi/sub-1_dir-j_dwi.bval b/.../data/buds/sub-1/dwi/sub-1_dir-j_dwi.bval → .../data/buds/sub-1/dwi/sub-1_dir-j_dwi.bval
diff --git a/.../data/buds/sub-1/dwi/sub-1_dir-j_dwi.bvec → .../data/buds/sub-1/dwi/sub-1_dir-j_dwi.bvec b/.../data/buds/sub-1/dwi/sub-1_dir-j_dwi.bvec → .../data/buds/sub-1/dwi/sub-1_dir-j_dwi.bvec
diff --git a/.../data/buds/sub-1/dwi/sub-1_dir-j_dwi.json → .../data/buds/sub-1/dwi/sub-1_dir-j_dwi.json b/.../data/buds/sub-1/dwi/sub-1_dir-j_dwi.json → .../data/buds/sub-1/dwi/sub-1_dir-j_dwi.json
diff --git a/...ata/buds/sub-1/dwi/sub-1_dir-j_dwi.nii.gz → ...ata/buds/sub-1/dwi/sub-1_dir-j_dwi.nii.gz b/...ata/buds/sub-1/dwi/sub-1_dir-j_dwi.nii.gz → ...ata/buds/sub-1/dwi/sub-1_dir-j_dwi.nii.gz
diff --git a/qsiprep/data/crossing_rois.nii.gz → qsirecon/data/crossing_rois.nii.gz b/qsiprep/data/crossing_rois.nii.gz → qsirecon/data/crossing_rois.nii.gz
diff --git a/qsiprep/data/eddy_params.json → qsirecon/data/eddy_params.json b/qsiprep/data/eddy_params.json → qsirecon/data/eddy_params.json
diff --git a/qsiprep/data/eddy_params_testing.json → qsirecon/data/eddy_params_testing.json b/qsiprep/data/eddy_params_testing.json → qsirecon/data/eddy_params_testing.json
diff --git a/qsiprep/data/epi_atlasbased_brainmask.json → qsirecon/data/epi_atlasbased_brainmask.json b/qsiprep/data/epi_atlasbased_brainmask.json → qsirecon/data/epi_atlasbased_brainmask.json
diff --git a/qsiprep/data/epi_registration_settings.json → qsirecon/data/epi_registration_settings.json b/qsiprep/data/epi_registration_settings.json → qsirecon/data/epi_registration_settings.json
diff --git a/qsiprep/data/fmap-any_registration.json → qsirecon/data/fmap-any_registration.json b/qsiprep/data/fmap-any_registration.json → qsirecon/data/fmap-any_registration.json
diff --git a/...p/data/fmap-any_registration_testing.json → ...n/data/fmap-any_registration_testing.json b/...p/data/fmap-any_registration_testing.json → ...n/data/fmap-any_registration_testing.json
diff --git a/qsiprep/data/freesurfer_to_qsiprep.json → qsirecon/data/freesurfer_to_qsiprep.json b/qsiprep/data/freesurfer_to_qsiprep.json → qsirecon/data/freesurfer_to_qsiprep.json
diff --git a/qsiprep/data/identitytransform.txt → qsirecon/data/identitytransform.txt b/qsiprep/data/identitytransform.txt → qsirecon/data/identitytransform.txt
diff --git a/qsiprep/data/intermodal_ACPC.json → qsirecon/data/intermodal_ACPC.json b/qsiprep/data/intermodal_ACPC.json → qsirecon/data/intermodal_ACPC.json
diff --git a/qsiprep/data/intermodal_ACPC_sloppy.json → qsirecon/data/intermodal_ACPC_sloppy.json b/qsiprep/data/intermodal_ACPC_sloppy.json → qsirecon/data/intermodal_ACPC_sloppy.json
diff --git a/qsiprep/data/intramodal_ACPC.json → qsirecon/data/intramodal_ACPC.json b/qsiprep/data/intramodal_ACPC.json → qsirecon/data/intramodal_ACPC.json
diff --git a/qsiprep/data/intramodal_ACPC_sloppy.json → qsirecon/data/intramodal_ACPC_sloppy.json b/qsiprep/data/intramodal_ACPC_sloppy.json → qsirecon/data/intramodal_ACPC_sloppy.json
diff --git a/qsiprep/data/intramodal_nonlinear.json → qsirecon/data/intramodal_nonlinear.json b/qsiprep/data/intramodal_nonlinear.json → qsirecon/data/intramodal_nonlinear.json
diff --git a/qsiprep/data/itkIdentityTransform.txt → qsirecon/data/itkIdentityTransform.txt b/qsiprep/data/itkIdentityTransform.txt → qsirecon/data/itkIdentityTransform.txt
diff --git a/qsiprep/data/lesion/dataset_description.json → ...econ/data/lesion/dataset_description.json b/qsiprep/data/lesion/dataset_description.json → ...econ/data/lesion/dataset_description.json
diff --git a/...p/data/lesion/sub-1/anat/sub-1_T1w.nii.gz → ...n/data/lesion/sub-1/anat/sub-1_T1w.nii.gz b/...p/data/lesion/sub-1/anat/sub-1_T1w.nii.gz → ...n/data/lesion/sub-1/anat/sub-1_T1w.nii.gz
diff --git a/.../sub-1/anat/sub-1_label-lesion_roi.nii.gz → .../sub-1/anat/sub-1_label-lesion_roi.nii.gz b/.../sub-1/anat/sub-1_label-lesion_roi.nii.gz → .../sub-1/anat/sub-1_label-lesion_roi.nii.gz
diff --git a/qsiprep/data/lesion/sub-1/dwi/sub-1_dwi.bval → ...econ/data/lesion/sub-1/dwi/sub-1_dwi.bval b/qsiprep/data/lesion/sub-1/dwi/sub-1_dwi.bval → ...econ/data/lesion/sub-1/dwi/sub-1_dwi.bval
diff --git a/qsiprep/data/lesion/sub-1/dwi/sub-1_dwi.bvec → ...econ/data/lesion/sub-1/dwi/sub-1_dwi.bvec b/qsiprep/data/lesion/sub-1/dwi/sub-1_dwi.bvec → ...econ/data/lesion/sub-1/dwi/sub-1_dwi.bvec
diff --git a/qsiprep/data/lesion/sub-1/dwi/sub-1_dwi.json → ...econ/data/lesion/sub-1/dwi/sub-1_dwi.json b/qsiprep/data/lesion/sub-1/dwi/sub-1_dwi.json → ...econ/data/lesion/sub-1/dwi/sub-1_dwi.json
diff --git a/...ep/data/lesion/sub-1/dwi/sub-1_dwi.nii.gz → ...on/data/lesion/sub-1/dwi/sub-1_dwi.nii.gz b/...ep/data/lesion/sub-1/dwi/sub-1_dwi.nii.gz → ...on/data/lesion/sub-1/dwi/sub-1_dwi.nii.gz
diff --git a/qsiprep/data/mni_1mm_t1w_lps.nii.gz → qsirecon/data/mni_1mm_t1w_lps.nii.gz b/qsiprep/data/mni_1mm_t1w_lps.nii.gz → qsirecon/data/mni_1mm_t1w_lps.nii.gz
diff --git a/qsiprep/data/mni_1mm_t1w_lps_brain.nii.gz → qsirecon/data/mni_1mm_t1w_lps_brain.nii.gz b/qsiprep/data/mni_1mm_t1w_lps_brain.nii.gz → qsirecon/data/mni_1mm_t1w_lps_brain.nii.gz
diff --git a/.../data/mni_1mm_t1w_lps_brain_infant.nii.gz → .../data/mni_1mm_t1w_lps_brain_infant.nii.gz b/.../data/mni_1mm_t1w_lps_brain_infant.nii.gz → .../data/mni_1mm_t1w_lps_brain_infant.nii.gz
diff --git a/...rep/data/mni_1mm_t1w_lps_brainmask.nii.gz → ...con/data/mni_1mm_t1w_lps_brainmask.nii.gz b/...rep/data/mni_1mm_t1w_lps_brainmask.nii.gz → ...con/data/mni_1mm_t1w_lps_brainmask.nii.gz
diff --git a/...a/mni_1mm_t1w_lps_brainmask_infant.nii.gz → ...a/mni_1mm_t1w_lps_brainmask_infant.nii.gz b/...a/mni_1mm_t1w_lps_brainmask_infant.nii.gz → ...a/mni_1mm_t1w_lps_brainmask_infant.nii.gz
diff --git a/qsiprep/data/mni_1mm_t1w_lps_infant.nii.gz → qsirecon/data/mni_1mm_t1w_lps_infant.nii.gz b/qsiprep/data/mni_1mm_t1w_lps_infant.nii.gz → qsirecon/data/mni_1mm_t1w_lps_infant.nii.gz
diff --git a/qsiprep/data/mni_1mm_t2w_lps.nii.gz → qsirecon/data/mni_1mm_t2w_lps.nii.gz b/qsiprep/data/mni_1mm_t2w_lps.nii.gz → qsirecon/data/mni_1mm_t2w_lps.nii.gz
diff --git a/qsiprep/data/mni_1mm_t2w_lps_brain.nii.gz → qsirecon/data/mni_1mm_t2w_lps_brain.nii.gz b/qsiprep/data/mni_1mm_t2w_lps_brain.nii.gz → qsirecon/data/mni_1mm_t2w_lps_brain.nii.gz
diff --git a/.../data/mni_1mm_t2w_lps_brain_infant.nii.gz → .../data/mni_1mm_t2w_lps_brain_infant.nii.gz b/.../data/mni_1mm_t2w_lps_brain_infant.nii.gz → .../data/mni_1mm_t2w_lps_brain_infant.nii.gz
diff --git a/qsiprep/data/mni_1mm_t2w_lps_infant.nii.gz → qsirecon/data/mni_1mm_t2w_lps_infant.nii.gz b/qsiprep/data/mni_1mm_t2w_lps_infant.nii.gz → qsirecon/data/mni_1mm_t2w_lps_infant.nii.gz
diff --git a/qsiprep/data/mni_lps_fmap_atlas.nii.gz → qsirecon/data/mni_lps_fmap_atlas.nii.gz b/qsiprep/data/mni_lps_fmap_atlas.nii.gz → qsirecon/data/mni_lps_fmap_atlas.nii.gz
diff --git a/qsiprep/data/odfs.mat → qsirecon/data/odfs.mat b/qsiprep/data/odfs.mat → qsirecon/data/odfs.mat
diff --git a/qsiprep/data/pipelines/TORTOISE.json → qsirecon/data/pipelines/TORTOISE.json b/qsiprep/data/pipelines/TORTOISE.json → qsirecon/data/pipelines/TORTOISE.json
diff --git a/qsiprep/data/pipelines/amico_noddi.json → qsirecon/data/pipelines/amico_noddi.json b/qsiprep/data/pipelines/amico_noddi.json → qsirecon/data/pipelines/amico_noddi.json
diff --git a/qsiprep/data/pipelines/csdsi_3dshore.json → qsirecon/data/pipelines/csdsi_3dshore.json b/qsiprep/data/pipelines/csdsi_3dshore.json → qsirecon/data/pipelines/csdsi_3dshore.json
diff --git a/qsiprep/data/pipelines/dipy_3dshore.json → qsirecon/data/pipelines/dipy_3dshore.json b/qsiprep/data/pipelines/dipy_3dshore.json → qsirecon/data/pipelines/dipy_3dshore.json
diff --git a/qsiprep/data/pipelines/dipy_dki.json → qsirecon/data/pipelines/dipy_dki.json b/qsiprep/data/pipelines/dipy_dki.json → qsirecon/data/pipelines/dipy_dki.json
diff --git a/qsiprep/data/pipelines/dipy_mapmri.json → qsirecon/data/pipelines/dipy_mapmri.json b/qsiprep/data/pipelines/dipy_mapmri.json → qsirecon/data/pipelines/dipy_mapmri.json
diff --git a/.../data/pipelines/dsi_studio_autotrack.json → .../data/pipelines/dsi_studio_autotrack.json b/.../data/pipelines/dsi_studio_autotrack.json → .../data/pipelines/dsi_studio_autotrack.json
diff --git a/qsiprep/data/pipelines/dsi_studio_gqi.json → qsirecon/data/pipelines/dsi_studio_gqi.json b/qsiprep/data/pipelines/dsi_studio_gqi.json → qsirecon/data/pipelines/dsi_studio_gqi.json
diff --git a/qsiprep/data/pipelines/hbcd_scalar_maps.json → ...econ/data/pipelines/hbcd_scalar_maps.json b/qsiprep/data/pipelines/hbcd_scalar_maps.json → ...econ/data/pipelines/hbcd_scalar_maps.json
diff --git a/...ines/mrtrix_multishell_msmt_ACT-fast.json → ...ines/mrtrix_multishell_msmt_ACT-fast.json b/...ines/mrtrix_multishell_msmt_ACT-fast.json → ...ines/mrtrix_multishell_msmt_ACT-fast.json
diff --git a/...ines/mrtrix_multishell_msmt_ACT-hsvs.json → ...ines/mrtrix_multishell_msmt_ACT-hsvs.json b/...ines/mrtrix_multishell_msmt_ACT-hsvs.json → ...ines/mrtrix_multishell_msmt_ACT-hsvs.json
diff --git a/...pelines/mrtrix_multishell_msmt_noACT.json → ...pelines/mrtrix_multishell_msmt_noACT.json b/...pelines/mrtrix_multishell_msmt_noACT.json → ...pelines/mrtrix_multishell_msmt_noACT.json
diff --git a/...ix_multishell_msmt_pyafq_tractometry.json → ...ix_multishell_msmt_pyafq_tractometry.json b/...ix_multishell_msmt_pyafq_tractometry.json → ...ix_multishell_msmt_pyafq_tractometry.json
diff --git a/...nes/mrtrix_singleshell_ss3t_ACT-fast.json → ...nes/mrtrix_singleshell_ss3t_ACT-fast.json b/...nes/mrtrix_singleshell_ss3t_ACT-fast.json → ...nes/mrtrix_singleshell_ss3t_ACT-fast.json
diff --git a/...nes/mrtrix_singleshell_ss3t_ACT-hsvs.json → ...nes/mrtrix_singleshell_ss3t_ACT-hsvs.json b/...nes/mrtrix_singleshell_ss3t_ACT-hsvs.json → ...nes/mrtrix_singleshell_ss3t_ACT-hsvs.json
diff --git a/...elines/mrtrix_singleshell_ss3t_noACT.json → ...elines/mrtrix_singleshell_ss3t_noACT.json b/...elines/mrtrix_singleshell_ss3t_noACT.json → ...elines/mrtrix_singleshell_ss3t_noACT.json
diff --git a/...data/pipelines/multishell_scalarfest.json → ...data/pipelines/multishell_scalarfest.json b/...data/pipelines/multishell_scalarfest.json → ...data/pipelines/multishell_scalarfest.json
diff --git a/...rep/data/pipelines/pyafq_tractometry.json → ...con/data/pipelines/pyafq_tractometry.json b/...rep/data/pipelines/pyafq_tractometry.json → ...con/data/pipelines/pyafq_tractometry.json
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diff --git a/qsiprep/interfaces/dsi_studio.py → qsirecon/interfaces/dsi_studio.py b/qsiprep/interfaces/dsi_studio.py → qsirecon/interfaces/dsi_studio.py
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diff --git a/qsiprep/tests/data/forrest_gump_outputs.txt → qsirecon/tests/data/forrest_gump_outputs.txt b/qsiprep/tests/data/forrest_gump_outputs.txt → qsirecon/tests/data/forrest_gump_outputs.txt
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diff --git a/qsiprep/tests/data/mrtrix3_recon_outputs.txt → ...econ/tests/data/mrtrix3_recon_outputs.txt b/qsiprep/tests/data/mrtrix3_recon_outputs.txt → ...econ/tests/data/mrtrix3_recon_outputs.txt
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diff --git a/qsiprep/tests/data/multi_t1w_outputs.txt → qsirecon/tests/data/multi_t1w_outputs.txt b/qsiprep/tests/data/multi_t1w_outputs.txt → qsirecon/tests/data/multi_t1w_outputs.txt
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diff --git a/...ata/pyafq_recon_full_optional_outputs.txt → ...ata/pyafq_recon_full_optional_outputs.txt b/...ata/pyafq_recon_full_optional_outputs.txt → ...ata/pyafq_recon_full_optional_outputs.txt
diff --git a/...p/tests/data/pyafq_recon_full_outputs.txt → ...n/tests/data/pyafq_recon_full_outputs.txt b/...p/tests/data/pyafq_recon_full_outputs.txt → ...n/tests/data/pyafq_recon_full_outputs.txt
diff --git a/qsiprep/tests/data/scalar_mapper_outputs.txt → ...econ/tests/data/scalar_mapper_outputs.txt b/qsiprep/tests/data/scalar_mapper_outputs.txt → ...econ/tests/data/scalar_mapper_outputs.txt
diff --git a/...rep/tests/data/tortoise_recon_outputs.txt → ...con/tests/data/tortoise_recon_outputs.txt b/...rep/tests/data/tortoise_recon_outputs.txt → ...con/tests/data/tortoise_recon_outputs.txt
diff --git a/qsiprep/tests/run_local_tests.py → qsirecon/tests/run_local_tests.py b/qsiprep/tests/run_local_tests.py → qsirecon/tests/run_local_tests.py
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diff --git a/qsiprep/utils/__init__.py → qsirecon/utils/__init__.py b/qsiprep/utils/__init__.py → qsirecon/utils/__init__.py
diff --git a/qsiprep/utils/atlases.py → qsirecon/utils/atlases.py b/qsiprep/utils/atlases.py → qsirecon/utils/atlases.py
diff --git a/qsiprep/utils/bids.py → qsirecon/utils/bids.py b/qsiprep/utils/bids.py → qsirecon/utils/bids.py
diff --git a/qsiprep/utils/brainsuite_shore.py → qsirecon/utils/brainsuite_shore.py b/qsiprep/utils/brainsuite_shore.py → qsirecon/utils/brainsuite_shore.py
diff --git a/qsiprep/utils/bspline.py → qsirecon/utils/bspline.py b/qsiprep/utils/bspline.py → qsirecon/utils/bspline.py
diff --git a/qsiprep/utils/debug.py → qsirecon/utils/debug.py b/qsiprep/utils/debug.py → qsirecon/utils/debug.py
diff --git a/qsiprep/utils/grouping.py → qsirecon/utils/grouping.py b/qsiprep/utils/grouping.py → qsirecon/utils/grouping.py
diff --git a/qsiprep/utils/ingress.py → qsirecon/utils/ingress.py b/qsiprep/utils/ingress.py → qsirecon/utils/ingress.py
diff --git a/qsiprep/utils/maths.pyx → qsirecon/utils/maths.pyx b/qsiprep/utils/maths.pyx → qsirecon/utils/maths.pyx
diff --git a/qsiprep/utils/misc.py → qsirecon/utils/misc.py b/qsiprep/utils/misc.py → qsirecon/utils/misc.py
diff --git a/qsiprep/utils/sentry.py → qsirecon/utils/sentry.py b/qsiprep/utils/sentry.py → qsirecon/utils/sentry.py
diff --git a/qsiprep/utils/shm.py → qsirecon/utils/shm.py b/qsiprep/utils/shm.py → qsirecon/utils/shm.py
diff --git a/qsiprep/utils/sloppy_recon.py → qsirecon/utils/sloppy_recon.py b/qsiprep/utils/sloppy_recon.py → qsirecon/utils/sloppy_recon.py
diff --git a/qsiprep/utils/testing.py → qsirecon/utils/testing.py b/qsiprep/utils/testing.py → qsirecon/utils/testing.py
diff --git a/qsiprep/viz/__init__.py → qsirecon/viz/__init__.py b/qsiprep/viz/__init__.py → qsirecon/viz/__init__.py
diff --git a/qsiprep/viz/config.json → qsirecon/viz/config.json b/qsiprep/viz/config.json → qsirecon/viz/config.json
diff --git a/qsiprep/viz/recon_config.json → qsirecon/viz/recon_config.json b/qsiprep/viz/recon_config.json → qsirecon/viz/recon_config.json
diff --git a/qsiprep/viz/report.tpl → qsirecon/viz/report.tpl b/qsiprep/viz/report.tpl → qsirecon/viz/report.tpl
diff --git a/qsiprep/viz/reports.py → qsirecon/viz/reports.py b/qsiprep/viz/reports.py → qsirecon/viz/reports.py
diff --git a/qsiprep/viz/utils.py → qsirecon/viz/utils.py b/qsiprep/viz/utils.py → qsirecon/viz/utils.py
diff --git a/qsiprep/workflows/__init__.py → qsirecon/workflows/__init__.py b/qsiprep/workflows/__init__.py → qsirecon/workflows/__init__.py
diff --git a/qsiprep/workflows/anatomical/__init__.py → qsirecon/workflows/anatomical/__init__.py b/qsiprep/workflows/anatomical/__init__.py → qsirecon/workflows/anatomical/__init__.py
diff --git a/qsiprep/workflows/anatomical/surface.py → qsirecon/workflows/anatomical/surface.py b/qsiprep/workflows/anatomical/surface.py → qsirecon/workflows/anatomical/surface.py
diff --git a/qsiprep/workflows/anatomical/volume.py → qsirecon/workflows/anatomical/volume.py b/qsiprep/workflows/anatomical/volume.py → qsirecon/workflows/anatomical/volume.py
diff --git a/qsiprep/workflows/base.py → qsirecon/workflows/base.py b/qsiprep/workflows/base.py → qsirecon/workflows/base.py
diff --git a/qsiprep/workflows/dwi/__init__.py → qsirecon/workflows/dwi/__init__.py b/qsiprep/workflows/dwi/__init__.py → qsirecon/workflows/dwi/__init__.py
diff --git a/qsiprep/workflows/dwi/base.py → qsirecon/workflows/dwi/base.py b/qsiprep/workflows/dwi/base.py → qsirecon/workflows/dwi/base.py
diff --git a/qsiprep/workflows/dwi/confounds.py → qsirecon/workflows/dwi/confounds.py b/qsiprep/workflows/dwi/confounds.py → qsirecon/workflows/dwi/confounds.py
diff --git a/qsiprep/workflows/dwi/derivatives.py → qsirecon/workflows/dwi/derivatives.py b/qsiprep/workflows/dwi/derivatives.py → qsirecon/workflows/dwi/derivatives.py
diff --git a/...p/workflows/dwi/distortion_group_merge.py → ...n/workflows/dwi/distortion_group_merge.py b/...p/workflows/dwi/distortion_group_merge.py → ...n/workflows/dwi/distortion_group_merge.py
diff --git a/qsiprep/workflows/dwi/finalize.py → qsirecon/workflows/dwi/finalize.py b/qsiprep/workflows/dwi/finalize.py → qsirecon/workflows/dwi/finalize.py
diff --git a/qsiprep/workflows/dwi/fsl.py → qsirecon/workflows/dwi/fsl.py b/qsiprep/workflows/dwi/fsl.py → qsirecon/workflows/dwi/fsl.py
diff --git a/qsiprep/workflows/dwi/hmc.py → qsirecon/workflows/dwi/hmc.py b/qsiprep/workflows/dwi/hmc.py → qsirecon/workflows/dwi/hmc.py
diff --git a/qsiprep/workflows/dwi/hmc_sdc.py → qsirecon/workflows/dwi/hmc_sdc.py b/qsiprep/workflows/dwi/hmc_sdc.py → qsirecon/workflows/dwi/hmc_sdc.py
diff --git a/qsiprep/workflows/dwi/intramodal_template.py → ...econ/workflows/dwi/intramodal_template.py b/qsiprep/workflows/dwi/intramodal_template.py → ...econ/workflows/dwi/intramodal_template.py
diff --git a/qsiprep/workflows/dwi/merge.py → qsirecon/workflows/dwi/merge.py b/qsiprep/workflows/dwi/merge.py → qsirecon/workflows/dwi/merge.py
diff --git a/qsiprep/workflows/dwi/pre_hmc.py → qsirecon/workflows/dwi/pre_hmc.py b/qsiprep/workflows/dwi/pre_hmc.py → qsirecon/workflows/dwi/pre_hmc.py
diff --git a/qsiprep/workflows/dwi/qc.py → qsirecon/workflows/dwi/qc.py b/qsiprep/workflows/dwi/qc.py → qsirecon/workflows/dwi/qc.py
diff --git a/qsiprep/workflows/dwi/registration.py → qsirecon/workflows/dwi/registration.py b/qsiprep/workflows/dwi/registration.py → qsirecon/workflows/dwi/registration.py
diff --git a/qsiprep/workflows/dwi/resampling.py → qsirecon/workflows/dwi/resampling.py b/qsiprep/workflows/dwi/resampling.py → qsirecon/workflows/dwi/resampling.py
diff --git a/qsiprep/workflows/dwi/util.py → qsirecon/workflows/dwi/util.py b/qsiprep/workflows/dwi/util.py → qsirecon/workflows/dwi/util.py
diff --git a/qsiprep/workflows/fieldmap/__init__.py → qsirecon/workflows/fieldmap/__init__.py b/qsiprep/workflows/fieldmap/__init__.py → qsirecon/workflows/fieldmap/__init__.py
diff --git a/qsiprep/workflows/fieldmap/base.py → qsirecon/workflows/fieldmap/base.py b/qsiprep/workflows/fieldmap/base.py → qsirecon/workflows/fieldmap/base.py
diff --git a/qsiprep/workflows/fieldmap/drbuddi.py → qsirecon/workflows/fieldmap/drbuddi.py b/qsiprep/workflows/fieldmap/drbuddi.py → qsirecon/workflows/fieldmap/drbuddi.py
diff --git a/qsiprep/workflows/fieldmap/fmap.py → qsirecon/workflows/fieldmap/fmap.py b/qsiprep/workflows/fieldmap/fmap.py → qsirecon/workflows/fieldmap/fmap.py
diff --git a/qsiprep/workflows/fieldmap/pepolar.py → qsirecon/workflows/fieldmap/pepolar.py b/qsiprep/workflows/fieldmap/pepolar.py → qsirecon/workflows/fieldmap/pepolar.py
diff --git a/qsiprep/workflows/fieldmap/phdiff.py → qsirecon/workflows/fieldmap/phdiff.py b/qsiprep/workflows/fieldmap/phdiff.py → qsirecon/workflows/fieldmap/phdiff.py
diff --git a/qsiprep/workflows/fieldmap/syn.py → qsirecon/workflows/fieldmap/syn.py b/qsiprep/workflows/fieldmap/syn.py → qsirecon/workflows/fieldmap/syn.py
diff --git a/qsiprep/workflows/fieldmap/unwarp.py → qsirecon/workflows/fieldmap/unwarp.py b/qsiprep/workflows/fieldmap/unwarp.py → qsirecon/workflows/fieldmap/unwarp.py
diff --git a/qsiprep/workflows/fieldmap/utils.py → qsirecon/workflows/fieldmap/utils.py b/qsiprep/workflows/fieldmap/utils.py → qsirecon/workflows/fieldmap/utils.py
diff --git a/qsiprep/workflows/recon/__init__.py → qsirecon/workflows/recon/__init__.py b/qsiprep/workflows/recon/__init__.py → qsirecon/workflows/recon/__init__.py
diff --git a/qsiprep/workflows/recon/amico.py → qsirecon/workflows/recon/amico.py b/qsiprep/workflows/recon/amico.py → qsirecon/workflows/recon/amico.py
diff --git a/qsiprep/workflows/recon/anatomical.py → qsirecon/workflows/recon/anatomical.py b/qsiprep/workflows/recon/anatomical.py → qsirecon/workflows/recon/anatomical.py
diff --git a/qsiprep/workflows/recon/base.py → qsirecon/workflows/recon/base.py b/qsiprep/workflows/recon/base.py → qsirecon/workflows/recon/base.py
diff --git a/qsiprep/workflows/recon/build_workflow.py → qsirecon/workflows/recon/build_workflow.py b/qsiprep/workflows/recon/build_workflow.py → qsirecon/workflows/recon/build_workflow.py
diff --git a/qsiprep/workflows/recon/converters.py → qsirecon/workflows/recon/converters.py b/qsiprep/workflows/recon/converters.py → qsirecon/workflows/recon/converters.py
diff --git a/qsiprep/workflows/recon/dipy.py → qsirecon/workflows/recon/dipy.py b/qsiprep/workflows/recon/dipy.py → qsirecon/workflows/recon/dipy.py
diff --git a/qsiprep/workflows/recon/dsi_studio.py → qsirecon/workflows/recon/dsi_studio.py b/qsiprep/workflows/recon/dsi_studio.py → qsirecon/workflows/recon/dsi_studio.py
diff --git a/qsiprep/workflows/recon/mrtrix.py → qsirecon/workflows/recon/mrtrix.py b/qsiprep/workflows/recon/mrtrix.py → qsirecon/workflows/recon/mrtrix.py
diff --git a/qsiprep/workflows/recon/pyafq.py → qsirecon/workflows/recon/pyafq.py b/qsiprep/workflows/recon/pyafq.py → qsirecon/workflows/recon/pyafq.py
diff --git a/qsiprep/workflows/recon/scalar_mapping.py → qsirecon/workflows/recon/scalar_mapping.py b/qsiprep/workflows/recon/scalar_mapping.py → qsirecon/workflows/recon/scalar_mapping.py
diff --git a/qsiprep/workflows/recon/steinhardt.py → qsirecon/workflows/recon/steinhardt.py b/qsiprep/workflows/recon/steinhardt.py → qsirecon/workflows/recon/steinhardt.py
diff --git a/qsiprep/workflows/recon/tortoise.py → qsirecon/workflows/recon/tortoise.py b/qsiprep/workflows/recon/tortoise.py → qsirecon/workflows/recon/tortoise.py
diff --git a/qsiprep/workflows/recon/utils.py → qsirecon/workflows/recon/utils.py b/qsiprep/workflows/recon/utils.py → qsirecon/workflows/recon/utils.py
diff --git a/qsiprep/workflows/reports.py → qsirecon/workflows/reports.py b/qsiprep/workflows/reports.py → qsirecon/workflows/reports.py
diff --git a/wrapper/qsiprep_container/__init__.py → wrapper/qsirecon_container/__init__.py b/wrapper/qsiprep_container/__init__.py → wrapper/qsirecon_container/__init__.py
diff --git a/wrapper/qsiprep_container/qsiprep_docker.py → wrapper/qsirecon_container/qsiprep_docker.py b/wrapper/qsiprep_container/qsiprep_docker.py → wrapper/qsirecon_container/qsiprep_docker.py
diff --git a/.../qsiprep_container/qsiprep_singularity.py → ...qsirecon_container/qsiprep_singularity.py b/.../qsiprep_container/qsiprep_singularity.py → ...qsirecon_container/qsiprep_singularity.py