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tsalotsalo
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Update expected outputs.
1 parent 0d0599b commit 0b88946

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-890
lines changed

‎xcp_d/interfaces/bids.py‎

Lines changed: 20 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -258,25 +258,30 @@ def _run_interface(self, runtime):
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atlas = self.inputs.atlas
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Sources = self.inputs.Sources
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261-
atlas_out_dir = os.path.join(output_dir, f'atlases/atlas-{atlas}')
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tpl = get_entity(name_source, 'tpl')
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res = get_entity(name_source, 'res')
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den = get_entity(name_source, 'den')
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cohort = get_entity(name_source, 'cohort')
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cohort_str = f'_cohort-{cohort}' if cohort else ''
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res_str = f'_res-{res}' if res else ''
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den_str = f'_den-{den}' if den else ''
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atlas_out_dir = os.path.join(output_dir, f'atlases/tpl-{tpl}')
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if cohort:
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atlas_out_dir = os.path.join(atlas_out_dir, f'cohort-{cohort}')
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if res:
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out_basename = f'tpl-{tpl}{cohort_str}_atlas-{atlas}{res_str}_dseg'
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else:
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out_basename = f'tpl-{tpl}{cohort_str}_atlas-{atlas}{den_str}_dseg'
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if in_file.endswith('.tsv'):
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out_basename = f'atlas-{atlas}_dseg'
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extension = '.tsv'
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elif in_file.endswith('.dlabel.nii'):
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extension = '.dlabel.nii'
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else:
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extension = '.nii.gz' if name_source.endswith('.nii.gz') else '.dlabel.nii'
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space = get_entity(name_source, 'space')
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res = get_entity(name_source, 'res')
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den = get_entity(name_source, 'den')
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cohort = get_entity(name_source, 'cohort')
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cohort_str = f'_cohort-{cohort}' if cohort else ''
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res_str = f'_res-{res}' if res else ''
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den_str = f'_den-{den}' if den else ''
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if extension == '.dlabel.nii':
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out_basename = f'atlas-{atlas}_space-{space}{den_str}{cohort_str}_dseg'
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elif extension == '.nii.gz':
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out_basename = f'atlas-{atlas}_space-{space}{res_str}{cohort_str}_dseg'
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extension = '.nii.gz'
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os.makedirs(atlas_out_dir, exist_ok=True)
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out_file = os.path.join(atlas_out_dir, f'{out_basename}{extension}')

‎xcp_d/tests/data/test_ds001419_cifti_outputs.txt‎

Lines changed: 168 additions & 166 deletions
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‎xcp_d/tests/data/test_ds001419_cifti_with_skip_outputs.txt‎

Lines changed: 136 additions & 134 deletions
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‎xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt‎

Lines changed: 44 additions & 42 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,16 @@
1-
atlases
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atlases/atlas-4S156Parcels
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atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.tsv
4-
atlases/atlas-4S156Parcels/atlas-4S156Parcels_space-MNI152NLin2009cAsym_dseg.json
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atlases/atlas-4S156Parcels/atlas-4S156Parcels_space-MNI152NLin2009cAsym_dseg.nii.gz
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atlases/atlas-Schaefer100
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atlases/atlas-Schaefer100/atlas-Schaefer100_dseg.tsv
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atlases/atlas-Schaefer100/atlas-Schaefer100_space-MNI152NLin2009cAsym_dseg.json
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atlases/atlas-Schaefer100/atlas-Schaefer100_space-MNI152NLin2009cAsym_dseg.nii.gz
10-
atlases/dataset_description.json
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dataset_description.json
2+
derivatives
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derivatives/atlases
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derivatives/atlases/atlas-4S156Parcels_description.json
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derivatives/atlases/atlas-Schaefer100_description.json
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derivatives/atlases/dataset_description.json
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derivatives/atlases/tpl-MNI152NLin2009cAsym
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derivatives/atlases/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_atlas-4S156Parcels_dseg.json
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derivatives/atlases/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_atlas-4S156Parcels_dseg.nii.gz
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derivatives/atlases/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_atlas-4S156Parcels_dseg.tsv
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derivatives/atlases/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_atlas-Schaefer100_dseg.json
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derivatives/atlases/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_atlas-Schaefer100_dseg.nii.gz
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derivatives/atlases/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_atlas-Schaefer100_dseg.tsv
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desc-linc_qc.json
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logs
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logs/CITATION.bib
@@ -26,27 +28,27 @@ sub-01/func/sub-01_task-mixedgamblestask_run-1_motion.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_motion.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_outliers.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_outliers.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-coverage_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-coverage_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-mean_timeseries.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-mean_timeseries.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-pearsoncorrelation_relmat.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-pearsoncorrelation_relmat.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-reho_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-reho_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-coverage_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-coverage_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-mean_timeseries.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-mean_timeseries.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-pearsoncorrelation_relmat.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-pearsoncorrelation_relmat.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-reho_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-reho_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_desc-denoisedSmoothed_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_desc-denoisedSmoothed_bold.nii.gz
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_desc-denoised_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_desc-denoised_bold.nii.gz
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_desc-linc_qc.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-coverage_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-coverage_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-mean_timeseries.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-mean_timeseries.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-pearsoncorrelation_relmat.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-pearsoncorrelation_relmat.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-reho_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-reho_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-Schaefer100_stat-coverage_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-Schaefer100_stat-coverage_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-Schaefer100_stat-mean_timeseries.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-Schaefer100_stat-mean_timeseries.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-Schaefer100_stat-pearsoncorrelation_relmat.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-Schaefer100_stat-pearsoncorrelation_relmat.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-Schaefer100_stat-reho_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_seg-Schaefer100_stat-reho_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_stat-reho_boldmap.json
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sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_stat-reho_boldmap.nii.gz
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sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-abcc_qc.hdf5
@@ -56,27 +58,27 @@ sub-01/func/sub-01_task-mixedgamblestask_run-2_motion.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_motion.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_outliers.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_outliers.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-coverage_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-coverage_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-mean_timeseries.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-mean_timeseries.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-pearsoncorrelation_relmat.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-pearsoncorrelation_relmat.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-reho_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-4S156Parcels_stat-reho_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-coverage_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-coverage_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-mean_timeseries.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-mean_timeseries.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-pearsoncorrelation_relmat.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-pearsoncorrelation_relmat.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-reho_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_atlas-Schaefer100_stat-reho_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_desc-denoisedSmoothed_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_desc-denoisedSmoothed_bold.nii.gz
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_desc-denoised_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_desc-denoised_bold.nii.gz
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_desc-linc_qc.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-coverage_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-coverage_bold.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-pearsoncorrelation_relmat.json
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sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_seg-4S156Parcels_stat-reho_bold.json
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sub-01/sub-01.html

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