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Move atlases into a subfolder #377

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merged 6 commits into from
Jan 4, 2024
Merged

Move atlases into a subfolder #377

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f8f11fc
Write out atlases to subfolder.
tsalo Dec 18, 2023
259ccea
Update expected outputs.
tsalo Dec 18, 2023
0b91773
Merge remote-tracking branch 'upstream/main' into move-atlases
tsalo Dec 18, 2023
5d06302
Merge remote-tracking branch 'upstream/main' into move-atlases
tsalo Dec 20, 2023
d656720
Merge remote-tracking branch 'upstream/main' into move-atlases
tsalo Jan 4, 2024
dc19115
Document the change.
tsalo Jan 4, 2024
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4 changes: 2 additions & 2 deletions aslprep/data/aslprep_bids_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@
],
"default_path_patterns": [
"[desc-{desc}_]{suffix<cbf>}{extension<.json>|.json}",
"[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dseg>}{extension<.nii|.nii.gz|.tsv|.json>|.nii.gz}",
"[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<dseg>}{extension<.dlabel.nii|.tsv|.json>|.dlabel.nii}",
"atlases/atlas-{atlas}/[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dseg>}{extension<.nii|.nii.gz|.tsv|.json>|.nii.gz}",
"atlases/atlas-{atlas}/[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<dseg>}{extension<.dlabel.nii|.tsv|.json>|.dlabel.nii}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}]_{suffix<defacemask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<bold|cbv|sbref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
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127 changes: 71 additions & 56 deletions aslprep/tests/data/expected_outputs_examples_pasl_multipld.txt
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@@ -1,65 +1,80 @@
atlas-4S1056Parcels_dseg.json
atlas-4S1056Parcels_dseg.tsv
atlas-4S156Parcels_dseg.json
atlas-4S156Parcels_dseg.tsv
atlas-4S256Parcels_dseg.json
atlas-4S256Parcels_dseg.tsv
atlas-4S356Parcels_dseg.json
atlas-4S356Parcels_dseg.tsv
atlas-4S456Parcels_dseg.json
atlas-4S456Parcels_dseg.tsv
atlas-4S556Parcels_dseg.json
atlas-4S556Parcels_dseg.tsv
atlas-4S656Parcels_dseg.json
atlas-4S656Parcels_dseg.tsv
atlas-4S756Parcels_dseg.json
atlas-4S756Parcels_dseg.tsv
atlas-4S856Parcels_dseg.json
atlas-4S856Parcels_dseg.tsv
atlas-4S956Parcels_dseg.json
atlas-4S956Parcels_dseg.tsv
atlas-Glasser_dseg.json
atlas-Glasser_dseg.tsv
atlas-Gordon_dseg.json
atlas-Gordon_dseg.tsv
atlas-HCP_dseg.json
atlas-HCP_dseg.tsv
atlas-Tian_dseg.json
atlas-Tian_dseg.tsv
atlases
atlases/atlas-4S1056Parcels
atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_dseg.json
atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_dseg.tsv
atlases/atlas-4S1056Parcels/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.json
atlases/atlas-4S1056Parcels/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.nii.gz
atlases/atlas-4S156Parcels
atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.json
atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.tsv
atlases/atlas-4S156Parcels/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.json
atlases/atlas-4S156Parcels/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.nii.gz
atlases/atlas-4S256Parcels
atlases/atlas-4S256Parcels/atlas-4S256Parcels_dseg.json
atlases/atlas-4S256Parcels/atlas-4S256Parcels_dseg.tsv
atlases/atlas-4S256Parcels/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.json
atlases/atlas-4S256Parcels/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.nii.gz
atlases/atlas-4S356Parcels
atlases/atlas-4S356Parcels/atlas-4S356Parcels_dseg.json
atlases/atlas-4S356Parcels/atlas-4S356Parcels_dseg.tsv
atlases/atlas-4S356Parcels/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.json
atlases/atlas-4S356Parcels/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.nii.gz
atlases/atlas-4S456Parcels
atlases/atlas-4S456Parcels/atlas-4S456Parcels_dseg.json
atlases/atlas-4S456Parcels/atlas-4S456Parcels_dseg.tsv
atlases/atlas-4S456Parcels/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.json
atlases/atlas-4S456Parcels/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz
atlases/atlas-4S556Parcels
atlases/atlas-4S556Parcels/atlas-4S556Parcels_dseg.json
atlases/atlas-4S556Parcels/atlas-4S556Parcels_dseg.tsv
atlases/atlas-4S556Parcels/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.json
atlases/atlas-4S556Parcels/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz
atlases/atlas-4S656Parcels
atlases/atlas-4S656Parcels/atlas-4S656Parcels_dseg.json
atlases/atlas-4S656Parcels/atlas-4S656Parcels_dseg.tsv
atlases/atlas-4S656Parcels/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.json
atlases/atlas-4S656Parcels/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz
atlases/atlas-4S756Parcels
atlases/atlas-4S756Parcels/atlas-4S756Parcels_dseg.json
atlases/atlas-4S756Parcels/atlas-4S756Parcels_dseg.tsv
atlases/atlas-4S756Parcels/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.json
atlases/atlas-4S756Parcels/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz
atlases/atlas-4S856Parcels
atlases/atlas-4S856Parcels/atlas-4S856Parcels_dseg.json
atlases/atlas-4S856Parcels/atlas-4S856Parcels_dseg.tsv
atlases/atlas-4S856Parcels/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.json
atlases/atlas-4S856Parcels/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz
atlases/atlas-4S956Parcels
atlases/atlas-4S956Parcels/atlas-4S956Parcels_dseg.json
atlases/atlas-4S956Parcels/atlas-4S956Parcels_dseg.tsv
atlases/atlas-4S956Parcels/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.json
atlases/atlas-4S956Parcels/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz
atlases/atlas-Glasser
atlases/atlas-Glasser/atlas-Glasser_dseg.json
atlases/atlas-Glasser/atlas-Glasser_dseg.tsv
atlases/atlas-Glasser/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.json
atlases/atlas-Glasser/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz
atlases/atlas-Gordon
atlases/atlas-Gordon/atlas-Gordon_dseg.json
atlases/atlas-Gordon/atlas-Gordon_dseg.tsv
atlases/atlas-Gordon/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.json
atlases/atlas-Gordon/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.nii.gz
atlases/atlas-HCP
atlases/atlas-HCP/atlas-HCP_dseg.json
atlases/atlas-HCP/atlas-HCP_dseg.tsv
atlases/atlas-HCP/space-MNI152NLin6Asym_atlas-HCP_res-02_dseg.json
atlases/atlas-HCP/space-MNI152NLin6Asym_atlas-HCP_res-02_dseg.nii.gz
atlases/atlas-Tian
atlases/atlas-Tian/atlas-Tian_dseg.json
atlases/atlas-Tian/atlas-Tian_dseg.tsv
atlases/atlas-Tian/space-MNI152NLin6Asym_atlas-Tian_res-02_dseg.json
atlases/atlas-Tian/space-MNI152NLin6Asym_atlas-Tian_res-02_dseg.nii.gz
desc-qualitycontrol_cbf.json
logs
logs/CITATION.bib
logs/CITATION.html
logs/CITATION.md
logs/CITATION.tex
space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.json
space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.json
space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-HCP_res-02_dseg.json
space-MNI152NLin6Asym_atlas-HCP_res-02_dseg.nii.gz
space-MNI152NLin6Asym_atlas-Tian_res-02_dseg.json
space-MNI152NLin6Asym_atlas-Tian_res-02_dseg.nii.gz
sub-01
sub-01.html
sub-01/ses-1
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127 changes: 71 additions & 56 deletions aslprep/tests/data/expected_outputs_examples_pcasl_multipld.txt
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@@ -1,65 +1,80 @@
atlas-4S1056Parcels_dseg.json
atlas-4S1056Parcels_dseg.tsv
atlas-4S156Parcels_dseg.json
atlas-4S156Parcels_dseg.tsv
atlas-4S256Parcels_dseg.json
atlas-4S256Parcels_dseg.tsv
atlas-4S356Parcels_dseg.json
atlas-4S356Parcels_dseg.tsv
atlas-4S456Parcels_dseg.json
atlas-4S456Parcels_dseg.tsv
atlas-4S556Parcels_dseg.json
atlas-4S556Parcels_dseg.tsv
atlas-4S656Parcels_dseg.json
atlas-4S656Parcels_dseg.tsv
atlas-4S756Parcels_dseg.json
atlas-4S756Parcels_dseg.tsv
atlas-4S856Parcels_dseg.json
atlas-4S856Parcels_dseg.tsv
atlas-4S956Parcels_dseg.json
atlas-4S956Parcels_dseg.tsv
atlas-Glasser_dseg.json
atlas-Glasser_dseg.tsv
atlas-Gordon_dseg.json
atlas-Gordon_dseg.tsv
atlas-HCP_dseg.json
atlas-HCP_dseg.tsv
atlas-Tian_dseg.json
atlas-Tian_dseg.tsv
atlases
atlases/atlas-4S1056Parcels
atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_dseg.json
atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_dseg.tsv
atlases/atlas-4S1056Parcels/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.json
atlases/atlas-4S1056Parcels/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.nii.gz
atlases/atlas-4S156Parcels
atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.json
atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.tsv
atlases/atlas-4S156Parcels/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.json
atlases/atlas-4S156Parcels/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.nii.gz
atlases/atlas-4S256Parcels
atlases/atlas-4S256Parcels/atlas-4S256Parcels_dseg.json
atlases/atlas-4S256Parcels/atlas-4S256Parcels_dseg.tsv
atlases/atlas-4S256Parcels/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.json
atlases/atlas-4S256Parcels/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.nii.gz
atlases/atlas-4S356Parcels
atlases/atlas-4S356Parcels/atlas-4S356Parcels_dseg.json
atlases/atlas-4S356Parcels/atlas-4S356Parcels_dseg.tsv
atlases/atlas-4S356Parcels/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.json
atlases/atlas-4S356Parcels/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.nii.gz
atlases/atlas-4S456Parcels
atlases/atlas-4S456Parcels/atlas-4S456Parcels_dseg.json
atlases/atlas-4S456Parcels/atlas-4S456Parcels_dseg.tsv
atlases/atlas-4S456Parcels/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.json
atlases/atlas-4S456Parcels/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz
atlases/atlas-4S556Parcels
atlases/atlas-4S556Parcels/atlas-4S556Parcels_dseg.json
atlases/atlas-4S556Parcels/atlas-4S556Parcels_dseg.tsv
atlases/atlas-4S556Parcels/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.json
atlases/atlas-4S556Parcels/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz
atlases/atlas-4S656Parcels
atlases/atlas-4S656Parcels/atlas-4S656Parcels_dseg.json
atlases/atlas-4S656Parcels/atlas-4S656Parcels_dseg.tsv
atlases/atlas-4S656Parcels/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.json
atlases/atlas-4S656Parcels/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz
atlases/atlas-4S756Parcels
atlases/atlas-4S756Parcels/atlas-4S756Parcels_dseg.json
atlases/atlas-4S756Parcels/atlas-4S756Parcels_dseg.tsv
atlases/atlas-4S756Parcels/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.json
atlases/atlas-4S756Parcels/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz
atlases/atlas-4S856Parcels
atlases/atlas-4S856Parcels/atlas-4S856Parcels_dseg.json
atlases/atlas-4S856Parcels/atlas-4S856Parcels_dseg.tsv
atlases/atlas-4S856Parcels/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.json
atlases/atlas-4S856Parcels/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz
atlases/atlas-4S956Parcels
atlases/atlas-4S956Parcels/atlas-4S956Parcels_dseg.json
atlases/atlas-4S956Parcels/atlas-4S956Parcels_dseg.tsv
atlases/atlas-4S956Parcels/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.json
atlases/atlas-4S956Parcels/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz
atlases/atlas-Glasser
atlases/atlas-Glasser/atlas-Glasser_dseg.json
atlases/atlas-Glasser/atlas-Glasser_dseg.tsv
atlases/atlas-Glasser/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.json
atlases/atlas-Glasser/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz
atlases/atlas-Gordon
atlases/atlas-Gordon/atlas-Gordon_dseg.json
atlases/atlas-Gordon/atlas-Gordon_dseg.tsv
atlases/atlas-Gordon/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.json
atlases/atlas-Gordon/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.nii.gz
atlases/atlas-HCP
atlases/atlas-HCP/atlas-HCP_dseg.json
atlases/atlas-HCP/atlas-HCP_dseg.tsv
atlases/atlas-HCP/space-MNI152NLin6Asym_atlas-HCP_res-02_dseg.json
atlases/atlas-HCP/space-MNI152NLin6Asym_atlas-HCP_res-02_dseg.nii.gz
atlases/atlas-Tian
atlases/atlas-Tian/atlas-Tian_dseg.json
atlases/atlas-Tian/atlas-Tian_dseg.tsv
atlases/atlas-Tian/space-MNI152NLin6Asym_atlas-Tian_res-02_dseg.json
atlases/atlas-Tian/space-MNI152NLin6Asym_atlas-Tian_res-02_dseg.nii.gz
desc-qualitycontrol_cbf.json
logs
logs/CITATION.bib
logs/CITATION.html
logs/CITATION.md
logs/CITATION.tex
space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.json
space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.json
space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.json
space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.nii.gz
space-MNI152NLin6Asym_atlas-HCP_res-02_dseg.json
space-MNI152NLin6Asym_atlas-HCP_res-02_dseg.nii.gz
space-MNI152NLin6Asym_atlas-Tian_res-02_dseg.json
space-MNI152NLin6Asym_atlas-Tian_res-02_dseg.nii.gz
sub-01
sub-01.html
sub-01/perf
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