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Drop volumetric Myers-Labonte atlas (PennLINC#1212)
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@tsalo
tsalo authored Jul 24, 2024
1 parent ff2ee5a commit 30c7e01
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Showing 7 changed files with 2 additions and 113 deletions.
2 changes: 1 addition & 1 deletion xcp_d/cli/parser.py
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Expand Up @@ -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."
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53 changes: 0 additions & 53 deletions xcp_d/data/atlases/tpl-MNI152NLin6Asym_atlas-MyersLabonte_desc-thresh50_dseg.json
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Binary file removed xcp_d/data/atlases/tpl-MNI152NLin6Asym_atlas-MyersLabonte_res-02_desc-thresh50_dseg.nii.gz
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20 changes: 0 additions & 20 deletions xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
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14 changes: 0 additions & 14 deletions xcp_d/tests/data/test_nibabies_outputs.txt
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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14 changes: 0 additions & 14 deletions xcp_d/tests/data/test_ukbiobank_outputs.txt
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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12 changes: 1 addition & 11 deletions xcp_d/utils/atlas.py
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Expand Up @@ -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
Expand Down Expand Up @@ -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}"))
Expand Down

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