diff --git a/xcp_d/cli/parser.py b/xcp_d/cli/parser.py index 7e5580058..d6d4ce0ec 100644 --- a/xcp_d/cli/parser.py +++ b/xcp_d/cli/parser.py @@ -1070,7 +1070,7 @@ def _validate_parameters(opts, build_log, parser): "--warp-surfaces-native2std is not supported for UK Biobank data." ) - for cifti_only_atlas in ["MIDB"]: + for cifti_only_atlas in ["MIDB", "MyersLabonte"]: if (cifti_only_atlas in opts.atlases) and (opts.file_format == "nifti"): build_log.warning( f"Atlas '{cifti_only_atlas}' requires CIFTI processing. Skipping atlas." diff --git a/xcp_d/data/atlases/tpl-MNI152NLin6Asym_atlas-MyersLabonte_desc-thresh50_dseg.json b/xcp_d/data/atlases/tpl-MNI152NLin6Asym_atlas-MyersLabonte_desc-thresh50_dseg.json deleted file mode 100644 index c59203fa0..000000000 --- a/xcp_d/data/atlases/tpl-MNI152NLin6Asym_atlas-MyersLabonte_desc-thresh50_dseg.json +++ /dev/null @@ -1,53 +0,0 @@ -{ - "BIDSVersion": "1.8.0", - "Description": "The 283-node Myers-Labonte infant atlas, thresholded and binarized at 50% probability.", - "Name": "Myers-Labonte infant atlas", - "ReferencesAndLinks": [ - "https://github.com/myersm0/myers-labonte_parcellation", - "https://doi.org/10.1093/cercor/bhae047" - ], - "Resolution": { - "02": { - "zooms": [ - 2.0, - 2.0, - 2.0 - ] - } - }, - "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz", - "cifti_label": { - "Description": "The region label present in the CIFTI file.", - "LongName": "CIFTI Label" - }, - "community": { - "Description": "The name of the community 'network' with which each parcel is associated.", - "LongName": "Community Label", - "Levels": { - "AntDefault": "Anterior default mode network", - "AntFrontoParietal": "Anterior fronto-parietal network", - "AntPreMotor": "Anterior pre-motor network", - "AntPrecuneus": "Anterior precuneus", - "Auditory": "Auditory network", - "Cingulate": "Cingulate network", - "DorsalAttn": "Dorsal attention network", - "InfFrontoParietal": "Inferior fronto-parietal network", - "InfMotor": "Inferior motor network", - "InfPrecuneus": "Inferior precuneus", - "Insula": "Insula", - "LatOrbitoFrontal": "Lateral orbito-frontal network", - "LateralVisual": "Lateral visual network", - "MedOrbitoFrontal": "Medial orbito-frontal network", - "MedialVisual": "Medial visual network", - "PostDefault": "Posterior default mode network", - "PostFrontoParietal": "Posterior fronto-parietal network", - "PostPreMotor": "Posterior pre-motor network", - "PreCentFrontoParietal": "Precentral fronto-parietal network", - "Salience": "Salience network", - "SupMotor": "Superior motor network", - "SupPrecuneus": "Superior precuneus", - "Unassigned": "No network assignment", - "VentralAttn": "Ventro-attention network" - } - } -} \ No newline at end of file diff --git a/xcp_d/data/atlases/tpl-MNI152NLin6Asym_atlas-MyersLabonte_res-02_desc-thresh50_dseg.nii.gz b/xcp_d/data/atlases/tpl-MNI152NLin6Asym_atlas-MyersLabonte_res-02_desc-thresh50_dseg.nii.gz deleted file mode 100644 index 4c13de9a9..000000000 Binary files a/xcp_d/data/atlases/tpl-MNI152NLin6Asym_atlas-MyersLabonte_res-02_desc-thresh50_dseg.nii.gz and /dev/null differ diff --git a/xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt b/xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt index 12d6d6242..6a5869b2b 100644 --- a/xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt +++ b/xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt @@ -51,10 +51,6 @@ atlases/atlas-HCP atlases/atlas-HCP/atlas-HCP_dseg.json atlases/atlas-HCP/atlas-HCP_dseg.tsv atlases/atlas-HCP/atlas-HCP_space-MNI152NLin2009cAsym_dseg.nii.gz -atlases/atlas-MyersLabonte -atlases/atlas-MyersLabonte/atlas-MyersLabonte_dseg.json -atlases/atlas-MyersLabonte/atlas-MyersLabonte_dseg.tsv -atlases/atlas-MyersLabonte/atlas-MyersLabonte_space-MNI152NLin2009cAsym_dseg.nii.gz atlases/atlas-Tian atlases/atlas-Tian/atlas-Tian_dseg.json atlases/atlas-Tian/atlas-Tian_dseg.tsv @@ -189,14 +185,6 @@ sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-HCP sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-HCP_stat-pearsoncorrelation_relmat.tsv sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-HCP_stat-reho_bold.json sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-HCP_stat-reho_bold.tsv -sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-coverage_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-coverage_bold.tsv -sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-mean_timeseries.json -sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-mean_timeseries.tsv -sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-pearsoncorrelation_relmat.json -sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-pearsoncorrelation_relmat.tsv -sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-reho_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-reho_bold.tsv sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-Tian_stat-coverage_bold.json sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-Tian_stat-coverage_bold.tsv sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-Tian_stat-mean_timeseries.json @@ -323,14 +311,6 @@ sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-HCP sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-HCP_stat-pearsoncorrelation_relmat.tsv sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-HCP_stat-reho_bold.json sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-HCP_stat-reho_bold.tsv -sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-coverage_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-coverage_bold.tsv -sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-mean_timeseries.json -sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-mean_timeseries.tsv -sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-pearsoncorrelation_relmat.json -sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-pearsoncorrelation_relmat.tsv -sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-reho_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-MyersLabonte_stat-reho_bold.tsv sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-Tian_stat-coverage_bold.json sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-Tian_stat-coverage_bold.tsv sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-Tian_stat-mean_timeseries.json diff --git a/xcp_d/tests/data/test_nibabies_outputs.txt b/xcp_d/tests/data/test_nibabies_outputs.txt index db2c6ad38..59b7a1143 100644 --- a/xcp_d/tests/data/test_nibabies_outputs.txt +++ b/xcp_d/tests/data/test_nibabies_outputs.txt @@ -51,10 +51,6 @@ atlases/atlas-HCP atlases/atlas-HCP/atlas-HCP_dseg.json atlases/atlas-HCP/atlas-HCP_dseg.tsv atlases/atlas-HCP/atlas-HCP_space-MNIInfant_cohort-1_dseg.nii.gz -atlases/atlas-MyersLabonte -atlases/atlas-MyersLabonte/atlas-MyersLabonte_dseg.json -atlases/atlas-MyersLabonte/atlas-MyersLabonte_dseg.tsv -atlases/atlas-MyersLabonte/atlas-MyersLabonte_space-MNIInfant_cohort-1_dseg.nii.gz atlases/atlas-Tian atlases/atlas-Tian/atlas-Tian_dseg.json atlases/atlas-Tian/atlas-Tian_dseg.tsv @@ -210,16 +206,6 @@ sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_coho sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-HCP_stat-pearsoncorrelation_relmat.tsv sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-HCP_stat-reho_bold.json sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-HCP_stat-reho_bold.tsv -sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-MyersLabonte_stat-alff_bold.json -sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-MyersLabonte_stat-alff_bold.tsv -sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-MyersLabonte_stat-coverage_bold.json -sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-MyersLabonte_stat-coverage_bold.tsv -sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-MyersLabonte_stat-mean_timeseries.json -sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-MyersLabonte_stat-mean_timeseries.tsv -sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-MyersLabonte_stat-pearsoncorrelation_relmat.json -sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-MyersLabonte_stat-pearsoncorrelation_relmat.tsv -sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-MyersLabonte_stat-reho_bold.json -sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-MyersLabonte_stat-reho_bold.tsv sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-Tian_stat-alff_bold.json sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-Tian_stat-alff_bold.tsv sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_seg-Tian_stat-coverage_bold.json diff --git a/xcp_d/tests/data/test_ukbiobank_outputs.txt b/xcp_d/tests/data/test_ukbiobank_outputs.txt index 68662554a..dd1f54d13 100644 --- a/xcp_d/tests/data/test_ukbiobank_outputs.txt +++ b/xcp_d/tests/data/test_ukbiobank_outputs.txt @@ -51,10 +51,6 @@ atlases/atlas-HCP atlases/atlas-HCP/atlas-HCP_dseg.json atlases/atlas-HCP/atlas-HCP_dseg.tsv atlases/atlas-HCP/atlas-HCP_space-MNI152NLin6Asym_dseg.nii.gz -atlases/atlas-MyersLabonte -atlases/atlas-MyersLabonte/atlas-MyersLabonte_dseg.json -atlases/atlas-MyersLabonte/atlas-MyersLabonte_dseg.tsv -atlases/atlas-MyersLabonte/atlas-MyersLabonte_space-MNI152NLin6Asym_dseg.nii.gz atlases/atlas-Tian atlases/atlas-Tian/atlas-Tian_dseg.json atlases/atlas-Tian/atlas-Tian_dseg.tsv @@ -215,16 +211,6 @@ sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-H sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-pearsoncorrelation_relmat.tsv sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-reho_bold.json sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-reho_bold.tsv -sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-MyersLabonte_stat-alff_bold.json -sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-MyersLabonte_stat-alff_bold.tsv -sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-MyersLabonte_stat-coverage_bold.json -sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-MyersLabonte_stat-coverage_bold.tsv -sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-MyersLabonte_stat-mean_timeseries.json -sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-MyersLabonte_stat-mean_timeseries.tsv -sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-MyersLabonte_stat-pearsoncorrelation_relmat.json -sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-MyersLabonte_stat-pearsoncorrelation_relmat.tsv -sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-MyersLabonte_stat-reho_bold.json -sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-MyersLabonte_stat-reho_bold.tsv sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-alff_bold.json sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-alff_bold.tsv sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-coverage_bold.json diff --git a/xcp_d/utils/atlas.py b/xcp_d/utils/atlas.py index c0c31339a..179b162a7 100644 --- a/xcp_d/utils/atlas.py +++ b/xcp_d/utils/atlas.py @@ -66,7 +66,7 @@ def get_atlas_nifti(atlas): atlas : {"4S156Parcels", "4S256Parcels", "4S356Parcels", "4S456Parcels", \ "4S556Parcels", "4S656Parcels", "4S756Parcels", "4S856Parcels", \ "4S956Parcels", "4S1056Parcels", "Glasser", "Gordon", \ - "Tian", "HCP", "MyersLabonte"} + "Tian", "HCP"} The name of the NIFTI atlas to fetch. Returns @@ -95,16 +95,6 @@ def get_atlas_nifti(atlas): atlas_file = join("/AtlasPack", atlas_fname) atlas_labels_file = join("/AtlasPack", tsv_fname) atlas_metadata_file = f"/AtlasPack/tpl-MNI152NLin6Asym_atlas-{atlas}_dseg.json" - elif "MyersLabonte" in atlas: - atlas_file = str( - load_data( - "atlases/tpl-MNI152NLin6Asym_atlas-MyersLabonte_res-02_desc-thresh50_dseg.nii.gz" - ) - ) - atlas_labels_file = str(load_data("atlases/atlas-MyersLabonte_desc-thresh50_dseg.tsv")) - atlas_metadata_file = str( - load_data("atlases/tpl-MNI152NLin6Asym_atlas-MyersLabonte_desc-thresh50_dseg.json") - ) else: atlas_file = str(load_data(f"atlases/{atlas_fname}")) atlas_labels_file = str(load_data(f"atlases/{tsv_fname}"))