From f8443e7858a12a253e629505aec122aff21a93ba Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Thu, 2 Nov 2023 09:01:31 -0400 Subject: [PATCH] Replace AtlasPack 0.0.5 atlases with AtlasPack 0.1.0 atlases (#334) * Fix path in run_local_tests.py. * Print the M0 filenames. * Use AtlasPack 0.1.0 atlases. * Update config.yml * Update the atlases. --- .circleci/config.yml | 2 +- Dockerfile | 2 +- ...xpected_outputs_examples_pasl_multipld.txt | 180 +++++++++--------- ...pected_outputs_examples_pcasl_multipld.txt | 140 +++++++------- ...ed_outputs_examples_pcasl_singlepld_ge.txt | 140 +++++++------- ...tputs_examples_pcasl_singlepld_philips.txt | 180 +++++++++--------- ...tputs_examples_pcasl_singlepld_siemens.txt | 140 +++++++------- .../tests/data/expected_outputs_test_001.txt | 140 +++++++------- .../tests/data/expected_outputs_test_002.txt | 100 +++++----- .../tests/data/expected_outputs_test_003.txt | 100 +++++----- aslprep/tests/run_local_tests.py | 4 +- aslprep/utils/atlas.py | 32 ++-- aslprep/utils/bids.py | 4 +- aslprep/workflows/asl/cbf.py | 13 +- docs/outputs.rst | 4 +- 15 files changed, 592 insertions(+), 589 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index d242497a2..d1086cdd0 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -4,7 +4,7 @@ orbs: .dockersetup: &dockersetup docker: - - image: pennlinc/aslprep_build:main + - image: pennlinc/aslprep_build:0.0.4 working_directory: /src/aslprep runinstall: &runinstall diff --git a/Dockerfile b/Dockerfile index 6fbfecdad..a8d0dabc7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM pennlinc/aslprep_build:0.0.3 +FROM pennlinc/aslprep_build:0.0.4 # Install aslprep COPY . /src/aslprep diff --git a/aslprep/tests/data/expected_outputs_examples_pasl_multipld.txt b/aslprep/tests/data/expected_outputs_examples_pasl_multipld.txt index 41a19fe72..f29e18c74 100644 --- a/aslprep/tests/data/expected_outputs_examples_pasl_multipld.txt +++ b/aslprep/tests/data/expected_outputs_examples_pasl_multipld.txt @@ -1,23 +1,23 @@ -aslprep/atlas-4S1052Parcels_dseg.json -aslprep/atlas-4S1052Parcels_dseg.tsv -aslprep/atlas-4S152Parcels_dseg.json -aslprep/atlas-4S152Parcels_dseg.tsv -aslprep/atlas-4S252Parcels_dseg.json -aslprep/atlas-4S252Parcels_dseg.tsv -aslprep/atlas-4S352Parcels_dseg.json -aslprep/atlas-4S352Parcels_dseg.tsv -aslprep/atlas-4S452Parcels_dseg.json -aslprep/atlas-4S452Parcels_dseg.tsv -aslprep/atlas-4S552Parcels_dseg.json -aslprep/atlas-4S552Parcels_dseg.tsv -aslprep/atlas-4S652Parcels_dseg.json -aslprep/atlas-4S652Parcels_dseg.tsv -aslprep/atlas-4S752Parcels_dseg.json -aslprep/atlas-4S752Parcels_dseg.tsv -aslprep/atlas-4S852Parcels_dseg.json -aslprep/atlas-4S852Parcels_dseg.tsv -aslprep/atlas-4S952Parcels_dseg.json -aslprep/atlas-4S952Parcels_dseg.tsv +aslprep/atlas-4S1056Parcels_dseg.json +aslprep/atlas-4S1056Parcels_dseg.tsv +aslprep/atlas-4S156Parcels_dseg.json +aslprep/atlas-4S156Parcels_dseg.tsv +aslprep/atlas-4S256Parcels_dseg.json +aslprep/atlas-4S256Parcels_dseg.tsv +aslprep/atlas-4S356Parcels_dseg.json +aslprep/atlas-4S356Parcels_dseg.tsv +aslprep/atlas-4S456Parcels_dseg.json +aslprep/atlas-4S456Parcels_dseg.tsv +aslprep/atlas-4S556Parcels_dseg.json +aslprep/atlas-4S556Parcels_dseg.tsv +aslprep/atlas-4S656Parcels_dseg.json +aslprep/atlas-4S656Parcels_dseg.tsv +aslprep/atlas-4S756Parcels_dseg.json +aslprep/atlas-4S756Parcels_dseg.tsv +aslprep/atlas-4S856Parcels_dseg.json +aslprep/atlas-4S856Parcels_dseg.tsv +aslprep/atlas-4S956Parcels_dseg.json +aslprep/atlas-4S956Parcels_dseg.tsv aslprep/atlas-Glasser_dseg.json aslprep/atlas-Glasser_dseg.tsv aslprep/atlas-Gordon_dseg.json @@ -32,26 +32,26 @@ aslprep/logs/CITATION.html aslprep/logs/CITATION.md aslprep/logs/CITATION.tex aslprep/qc.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S152Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S152Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S252Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S252Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S352Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S352Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S452Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S452Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S552Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S552Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S652Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S652Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S752Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S752Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S852Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S852Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S952Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S952Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.json aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz aslprep/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.json @@ -66,56 +66,56 @@ aslprep/sub-01/ses-BAS1 aslprep/sub-01/ses-BAS1/perf aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_aslref.json 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+aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-4S956Parcels_cbf.tsv +aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-4S956Parcels_desc-basilGM_cbf.tsv +aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-4S956Parcels_desc-basil_cbf.tsv +aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-4S956Parcels_desc-score_cbf.tsv +aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-4S956Parcels_desc-scrub_cbf.tsv aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-Glasser_cbf.tsv aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-Glasser_desc-basilGM_cbf.tsv aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-Glasser_desc-basil_cbf.tsv diff --git a/aslprep/tests/data/expected_outputs_examples_pcasl_multipld.txt b/aslprep/tests/data/expected_outputs_examples_pcasl_multipld.txt index 8e98c9037..0c99096eb 100644 --- a/aslprep/tests/data/expected_outputs_examples_pcasl_multipld.txt +++ b/aslprep/tests/data/expected_outputs_examples_pcasl_multipld.txt @@ -1,23 +1,23 @@ -aslprep/atlas-4S1052Parcels_dseg.json -aslprep/atlas-4S1052Parcels_dseg.tsv -aslprep/atlas-4S152Parcels_dseg.json -aslprep/atlas-4S152Parcels_dseg.tsv -aslprep/atlas-4S252Parcels_dseg.json -aslprep/atlas-4S252Parcels_dseg.tsv -aslprep/atlas-4S352Parcels_dseg.json -aslprep/atlas-4S352Parcels_dseg.tsv -aslprep/atlas-4S452Parcels_dseg.json -aslprep/atlas-4S452Parcels_dseg.tsv -aslprep/atlas-4S552Parcels_dseg.json -aslprep/atlas-4S552Parcels_dseg.tsv -aslprep/atlas-4S652Parcels_dseg.json -aslprep/atlas-4S652Parcels_dseg.tsv -aslprep/atlas-4S752Parcels_dseg.json -aslprep/atlas-4S752Parcels_dseg.tsv -aslprep/atlas-4S852Parcels_dseg.json -aslprep/atlas-4S852Parcels_dseg.tsv -aslprep/atlas-4S952Parcels_dseg.json -aslprep/atlas-4S952Parcels_dseg.tsv +aslprep/atlas-4S1056Parcels_dseg.json +aslprep/atlas-4S1056Parcels_dseg.tsv +aslprep/atlas-4S156Parcels_dseg.json +aslprep/atlas-4S156Parcels_dseg.tsv +aslprep/atlas-4S256Parcels_dseg.json +aslprep/atlas-4S256Parcels_dseg.tsv +aslprep/atlas-4S356Parcels_dseg.json +aslprep/atlas-4S356Parcels_dseg.tsv +aslprep/atlas-4S456Parcels_dseg.json +aslprep/atlas-4S456Parcels_dseg.tsv +aslprep/atlas-4S556Parcels_dseg.json +aslprep/atlas-4S556Parcels_dseg.tsv +aslprep/atlas-4S656Parcels_dseg.json +aslprep/atlas-4S656Parcels_dseg.tsv +aslprep/atlas-4S756Parcels_dseg.json +aslprep/atlas-4S756Parcels_dseg.tsv +aslprep/atlas-4S856Parcels_dseg.json +aslprep/atlas-4S856Parcels_dseg.tsv +aslprep/atlas-4S956Parcels_dseg.json +aslprep/atlas-4S956Parcels_dseg.tsv aslprep/atlas-Glasser_dseg.json aslprep/atlas-Glasser_dseg.tsv aslprep/atlas-Gordon_dseg.json @@ -32,26 +32,26 @@ aslprep/logs/CITATION.html aslprep/logs/CITATION.md aslprep/logs/CITATION.tex aslprep/qc.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S152Parcels_res-01_dseg.json 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+aslprep/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.json aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz aslprep/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.json @@ -65,36 +65,36 @@ aslprep/sub-01.html aslprep/sub-01/perf aslprep/sub-01/perf/sub-01_aslref.json aslprep/sub-01/perf/sub-01_aslref.nii.gz -aslprep/sub-01/perf/sub-01_atlas-4S1052Parcels_cbf.tsv 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+aslprep/sub-01/perf/sub-01_atlas-4S556Parcels_desc-basilGM_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S556Parcels_desc-basil_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S656Parcels_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S656Parcels_desc-basilGM_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S656Parcels_desc-basil_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S756Parcels_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S756Parcels_desc-basilGM_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S756Parcels_desc-basil_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S856Parcels_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S856Parcels_desc-basilGM_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S856Parcels_desc-basil_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S956Parcels_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S956Parcels_desc-basilGM_cbf.tsv +aslprep/sub-01/perf/sub-01_atlas-4S956Parcels_desc-basil_cbf.tsv aslprep/sub-01/perf/sub-01_atlas-Glasser_cbf.tsv aslprep/sub-01/perf/sub-01_atlas-Glasser_desc-basilGM_cbf.tsv aslprep/sub-01/perf/sub-01_atlas-Glasser_desc-basil_cbf.tsv diff --git a/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_ge.txt b/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_ge.txt index db9b1aa69..41c70c719 100644 --- a/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_ge.txt +++ b/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_ge.txt @@ -1,23 +1,23 @@ -aslprep/atlas-4S1052Parcels_dseg.json -aslprep/atlas-4S1052Parcels_dseg.tsv -aslprep/atlas-4S152Parcels_dseg.json -aslprep/atlas-4S152Parcels_dseg.tsv -aslprep/atlas-4S252Parcels_dseg.json -aslprep/atlas-4S252Parcels_dseg.tsv -aslprep/atlas-4S352Parcels_dseg.json -aslprep/atlas-4S352Parcels_dseg.tsv -aslprep/atlas-4S452Parcels_dseg.json -aslprep/atlas-4S452Parcels_dseg.tsv -aslprep/atlas-4S552Parcels_dseg.json -aslprep/atlas-4S552Parcels_dseg.tsv -aslprep/atlas-4S652Parcels_dseg.json -aslprep/atlas-4S652Parcels_dseg.tsv -aslprep/atlas-4S752Parcels_dseg.json -aslprep/atlas-4S752Parcels_dseg.tsv -aslprep/atlas-4S852Parcels_dseg.json -aslprep/atlas-4S852Parcels_dseg.tsv -aslprep/atlas-4S952Parcels_dseg.json -aslprep/atlas-4S952Parcels_dseg.tsv +aslprep/atlas-4S1056Parcels_dseg.json +aslprep/atlas-4S1056Parcels_dseg.tsv +aslprep/atlas-4S156Parcels_dseg.json +aslprep/atlas-4S156Parcels_dseg.tsv +aslprep/atlas-4S256Parcels_dseg.json +aslprep/atlas-4S256Parcels_dseg.tsv +aslprep/atlas-4S356Parcels_dseg.json +aslprep/atlas-4S356Parcels_dseg.tsv +aslprep/atlas-4S456Parcels_dseg.json +aslprep/atlas-4S456Parcels_dseg.tsv +aslprep/atlas-4S556Parcels_dseg.json +aslprep/atlas-4S556Parcels_dseg.tsv +aslprep/atlas-4S656Parcels_dseg.json +aslprep/atlas-4S656Parcels_dseg.tsv +aslprep/atlas-4S756Parcels_dseg.json +aslprep/atlas-4S756Parcels_dseg.tsv +aslprep/atlas-4S856Parcels_dseg.json +aslprep/atlas-4S856Parcels_dseg.tsv +aslprep/atlas-4S956Parcels_dseg.json +aslprep/atlas-4S956Parcels_dseg.tsv aslprep/atlas-Glasser_dseg.json aslprep/atlas-Glasser_dseg.tsv aslprep/atlas-Gordon_dseg.json @@ -32,26 +32,26 @@ aslprep/logs/CITATION.html aslprep/logs/CITATION.md aslprep/logs/CITATION.tex aslprep/qc.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S152Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S152Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S252Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S252Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S352Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S352Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S452Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S452Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S552Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S552Parcels_res-01_dseg.nii.gz 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aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.json aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz aslprep/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.json @@ -66,36 +66,36 @@ aslprep/sub-103/ses-ge3d aslprep/sub-103/ses-ge3d/perf aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_aslref.json aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_aslref.nii.gz -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-4S1052Parcels_cbf.tsv -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-4S1052Parcels_desc-basilGM_cbf.tsv -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-4S1052Parcels_desc-basil_cbf.tsv -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-4S152Parcels_cbf.tsv -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-4S152Parcels_desc-basilGM_cbf.tsv -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-4S152Parcels_desc-basil_cbf.tsv -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-4S252Parcels_cbf.tsv 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b/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_philips.txt @@ -1,23 +1,23 @@ -aslprep/atlas-4S1052Parcels_dseg.json -aslprep/atlas-4S1052Parcels_dseg.tsv -aslprep/atlas-4S152Parcels_dseg.json -aslprep/atlas-4S152Parcels_dseg.tsv -aslprep/atlas-4S252Parcels_dseg.json -aslprep/atlas-4S252Parcels_dseg.tsv -aslprep/atlas-4S352Parcels_dseg.json -aslprep/atlas-4S352Parcels_dseg.tsv -aslprep/atlas-4S452Parcels_dseg.json -aslprep/atlas-4S452Parcels_dseg.tsv -aslprep/atlas-4S552Parcels_dseg.json -aslprep/atlas-4S552Parcels_dseg.tsv -aslprep/atlas-4S652Parcels_dseg.json -aslprep/atlas-4S652Parcels_dseg.tsv -aslprep/atlas-4S752Parcels_dseg.json -aslprep/atlas-4S752Parcels_dseg.tsv -aslprep/atlas-4S852Parcels_dseg.json -aslprep/atlas-4S852Parcels_dseg.tsv -aslprep/atlas-4S952Parcels_dseg.json -aslprep/atlas-4S952Parcels_dseg.tsv +aslprep/atlas-4S1056Parcels_dseg.json +aslprep/atlas-4S1056Parcels_dseg.tsv +aslprep/atlas-4S156Parcels_dseg.json +aslprep/atlas-4S156Parcels_dseg.tsv +aslprep/atlas-4S256Parcels_dseg.json +aslprep/atlas-4S256Parcels_dseg.tsv +aslprep/atlas-4S356Parcels_dseg.json +aslprep/atlas-4S356Parcels_dseg.tsv +aslprep/atlas-4S456Parcels_dseg.json +aslprep/atlas-4S456Parcels_dseg.tsv +aslprep/atlas-4S556Parcels_dseg.json +aslprep/atlas-4S556Parcels_dseg.tsv +aslprep/atlas-4S656Parcels_dseg.json +aslprep/atlas-4S656Parcels_dseg.tsv +aslprep/atlas-4S756Parcels_dseg.json +aslprep/atlas-4S756Parcels_dseg.tsv +aslprep/atlas-4S856Parcels_dseg.json +aslprep/atlas-4S856Parcels_dseg.tsv +aslprep/atlas-4S956Parcels_dseg.json +aslprep/atlas-4S956Parcels_dseg.tsv aslprep/atlas-Glasser_dseg.json aslprep/atlas-Glasser_dseg.tsv aslprep/atlas-Gordon_dseg.json @@ -32,26 +32,26 @@ aslprep/logs/CITATION.html aslprep/logs/CITATION.md aslprep/logs/CITATION.tex aslprep/qc.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.nii.gz 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+aslprep/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.json aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz aslprep/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.json @@ -66,56 +66,56 @@ aslprep/sub-103/ses-philips2d aslprep/sub-103/ses-philips2d/perf aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_aslref.json aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_aslref.nii.gz -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-4S1052Parcels_cbf.tsv -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-4S1052Parcels_desc-basilGM_cbf.tsv -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-4S1052Parcels_desc-basil_cbf.tsv -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-4S1052Parcels_desc-score_cbf.tsv -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-4S1052Parcels_desc-scrub_cbf.tsv -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-4S152Parcels_cbf.tsv -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-4S152Parcels_desc-basilGM_cbf.tsv -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-4S152Parcels_desc-basil_cbf.tsv -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-4S152Parcels_desc-score_cbf.tsv 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+aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-4S956Parcels_desc-scrub_cbf.tsv aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-Glasser_cbf.tsv aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-Glasser_desc-basilGM_cbf.tsv aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-Glasser_desc-basil_cbf.tsv diff --git a/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_siemens.txt b/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_siemens.txt index c7f82f761..f79b63872 100644 --- a/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_siemens.txt +++ b/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_siemens.txt @@ -1,23 +1,23 @@ -aslprep/atlas-4S1052Parcels_dseg.json -aslprep/atlas-4S1052Parcels_dseg.tsv -aslprep/atlas-4S152Parcels_dseg.json -aslprep/atlas-4S152Parcels_dseg.tsv -aslprep/atlas-4S252Parcels_dseg.json -aslprep/atlas-4S252Parcels_dseg.tsv -aslprep/atlas-4S352Parcels_dseg.json -aslprep/atlas-4S352Parcels_dseg.tsv -aslprep/atlas-4S452Parcels_dseg.json -aslprep/atlas-4S452Parcels_dseg.tsv -aslprep/atlas-4S552Parcels_dseg.json -aslprep/atlas-4S552Parcels_dseg.tsv -aslprep/atlas-4S652Parcels_dseg.json -aslprep/atlas-4S652Parcels_dseg.tsv -aslprep/atlas-4S752Parcels_dseg.json -aslprep/atlas-4S752Parcels_dseg.tsv -aslprep/atlas-4S852Parcels_dseg.json -aslprep/atlas-4S852Parcels_dseg.tsv -aslprep/atlas-4S952Parcels_dseg.json -aslprep/atlas-4S952Parcels_dseg.tsv +aslprep/atlas-4S1056Parcels_dseg.json +aslprep/atlas-4S1056Parcels_dseg.tsv +aslprep/atlas-4S156Parcels_dseg.json +aslprep/atlas-4S156Parcels_dseg.tsv +aslprep/atlas-4S256Parcels_dseg.json +aslprep/atlas-4S256Parcels_dseg.tsv +aslprep/atlas-4S356Parcels_dseg.json +aslprep/atlas-4S356Parcels_dseg.tsv +aslprep/atlas-4S456Parcels_dseg.json +aslprep/atlas-4S456Parcels_dseg.tsv +aslprep/atlas-4S556Parcels_dseg.json +aslprep/atlas-4S556Parcels_dseg.tsv +aslprep/atlas-4S656Parcels_dseg.json +aslprep/atlas-4S656Parcels_dseg.tsv +aslprep/atlas-4S756Parcels_dseg.json +aslprep/atlas-4S756Parcels_dseg.tsv +aslprep/atlas-4S856Parcels_dseg.json +aslprep/atlas-4S856Parcels_dseg.tsv +aslprep/atlas-4S956Parcels_dseg.json +aslprep/atlas-4S956Parcels_dseg.tsv aslprep/atlas-Glasser_dseg.json aslprep/atlas-Glasser_dseg.tsv aslprep/atlas-Gordon_dseg.json @@ -32,26 +32,26 @@ aslprep/logs/CITATION.html aslprep/logs/CITATION.md aslprep/logs/CITATION.tex aslprep/qc.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S152Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S152Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S252Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S252Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S352Parcels_res-01_dseg.json 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aslprep/sub-103/ses-siemens3d/perf/sub-103_ses-siemens3d_atlas-Glasser_desc-basil_cbf.tsv diff --git a/aslprep/tests/data/expected_outputs_test_001.txt b/aslprep/tests/data/expected_outputs_test_001.txt index deaa2d096..d609ce1c2 100644 --- a/aslprep/tests/data/expected_outputs_test_001.txt +++ b/aslprep/tests/data/expected_outputs_test_001.txt @@ -1,23 +1,23 @@ -aslprep/atlas-4S1052Parcels_dseg.json -aslprep/atlas-4S1052Parcels_dseg.tsv -aslprep/atlas-4S152Parcels_dseg.json -aslprep/atlas-4S152Parcels_dseg.tsv -aslprep/atlas-4S252Parcels_dseg.json -aslprep/atlas-4S252Parcels_dseg.tsv -aslprep/atlas-4S352Parcels_dseg.json -aslprep/atlas-4S352Parcels_dseg.tsv -aslprep/atlas-4S452Parcels_dseg.json -aslprep/atlas-4S452Parcels_dseg.tsv -aslprep/atlas-4S552Parcels_dseg.json -aslprep/atlas-4S552Parcels_dseg.tsv -aslprep/atlas-4S652Parcels_dseg.json -aslprep/atlas-4S652Parcels_dseg.tsv -aslprep/atlas-4S752Parcels_dseg.json -aslprep/atlas-4S752Parcels_dseg.tsv 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+aslprep/sub-01/perf/sub-01_atlas-4S956Parcels_desc-scrub_cbf.tsv aslprep/sub-01/perf/sub-01_atlas-Glasser_cbf.tsv aslprep/sub-01/perf/sub-01_atlas-Glasser_desc-score_cbf.tsv aslprep/sub-01/perf/sub-01_atlas-Glasser_desc-scrub_cbf.tsv diff --git a/aslprep/tests/data/expected_outputs_test_002.txt b/aslprep/tests/data/expected_outputs_test_002.txt index 6df3e7898..a18deddfa 100644 --- a/aslprep/tests/data/expected_outputs_test_002.txt +++ b/aslprep/tests/data/expected_outputs_test_002.txt @@ -1,23 +1,23 @@ -aslprep/atlas-4S1052Parcels_dseg.json -aslprep/atlas-4S1052Parcels_dseg.tsv -aslprep/atlas-4S152Parcels_dseg.json -aslprep/atlas-4S152Parcels_dseg.tsv -aslprep/atlas-4S252Parcels_dseg.json -aslprep/atlas-4S252Parcels_dseg.tsv -aslprep/atlas-4S352Parcels_dseg.json -aslprep/atlas-4S352Parcels_dseg.tsv -aslprep/atlas-4S452Parcels_dseg.json -aslprep/atlas-4S452Parcels_dseg.tsv -aslprep/atlas-4S552Parcels_dseg.json -aslprep/atlas-4S552Parcels_dseg.tsv -aslprep/atlas-4S652Parcels_dseg.json -aslprep/atlas-4S652Parcels_dseg.tsv -aslprep/atlas-4S752Parcels_dseg.json -aslprep/atlas-4S752Parcels_dseg.tsv -aslprep/atlas-4S852Parcels_dseg.json -aslprep/atlas-4S852Parcels_dseg.tsv -aslprep/atlas-4S952Parcels_dseg.json -aslprep/atlas-4S952Parcels_dseg.tsv +aslprep/atlas-4S1056Parcels_dseg.json +aslprep/atlas-4S1056Parcels_dseg.tsv +aslprep/atlas-4S156Parcels_dseg.json +aslprep/atlas-4S156Parcels_dseg.tsv +aslprep/atlas-4S256Parcels_dseg.json +aslprep/atlas-4S256Parcels_dseg.tsv +aslprep/atlas-4S356Parcels_dseg.json +aslprep/atlas-4S356Parcels_dseg.tsv +aslprep/atlas-4S456Parcels_dseg.json +aslprep/atlas-4S456Parcels_dseg.tsv +aslprep/atlas-4S556Parcels_dseg.json +aslprep/atlas-4S556Parcels_dseg.tsv +aslprep/atlas-4S656Parcels_dseg.json +aslprep/atlas-4S656Parcels_dseg.tsv +aslprep/atlas-4S756Parcels_dseg.json +aslprep/atlas-4S756Parcels_dseg.tsv +aslprep/atlas-4S856Parcels_dseg.json +aslprep/atlas-4S856Parcels_dseg.tsv +aslprep/atlas-4S956Parcels_dseg.json +aslprep/atlas-4S956Parcels_dseg.tsv aslprep/atlas-Glasser_dseg.json aslprep/atlas-Glasser_dseg.tsv aslprep/atlas-Gordon_dseg.json @@ -32,26 +32,26 @@ aslprep/logs/CITATION.html aslprep/logs/CITATION.md aslprep/logs/CITATION.tex aslprep/qc.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S152Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S152Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S252Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S252Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S352Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S352Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S452Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S452Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S552Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S552Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S652Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S652Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S752Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S752Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S852Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S852Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S952Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S952Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.json aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz aslprep/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.json @@ -65,16 +65,16 @@ aslprep/sub-10R01383.html aslprep/sub-10R01383/perf aslprep/sub-10R01383/perf/sub-10R01383_aslref.json aslprep/sub-10R01383/perf/sub-10R01383_aslref.nii.gz -aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S1052Parcels_cbf.tsv -aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S152Parcels_cbf.tsv -aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S252Parcels_cbf.tsv -aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S352Parcels_cbf.tsv -aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S452Parcels_cbf.tsv -aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S552Parcels_cbf.tsv -aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S652Parcels_cbf.tsv -aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S752Parcels_cbf.tsv -aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S852Parcels_cbf.tsv -aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S952Parcels_cbf.tsv +aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S1056Parcels_cbf.tsv +aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S156Parcels_cbf.tsv +aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S256Parcels_cbf.tsv +aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S356Parcels_cbf.tsv +aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S456Parcels_cbf.tsv +aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S556Parcels_cbf.tsv +aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S656Parcels_cbf.tsv +aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S756Parcels_cbf.tsv +aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S856Parcels_cbf.tsv +aslprep/sub-10R01383/perf/sub-10R01383_atlas-4S956Parcels_cbf.tsv aslprep/sub-10R01383/perf/sub-10R01383_atlas-Glasser_cbf.tsv aslprep/sub-10R01383/perf/sub-10R01383_atlas-Gordon_cbf.tsv aslprep/sub-10R01383/perf/sub-10R01383_atlas-HCP_cbf.tsv diff --git a/aslprep/tests/data/expected_outputs_test_003.txt b/aslprep/tests/data/expected_outputs_test_003.txt index 034dc1b7a..5ca3b6f74 100644 --- a/aslprep/tests/data/expected_outputs_test_003.txt +++ b/aslprep/tests/data/expected_outputs_test_003.txt @@ -1,23 +1,23 @@ -aslprep/atlas-4S1052Parcels_dseg.json -aslprep/atlas-4S1052Parcels_dseg.tsv -aslprep/atlas-4S152Parcels_dseg.json -aslprep/atlas-4S152Parcels_dseg.tsv -aslprep/atlas-4S252Parcels_dseg.json -aslprep/atlas-4S252Parcels_dseg.tsv -aslprep/atlas-4S352Parcels_dseg.json -aslprep/atlas-4S352Parcels_dseg.tsv -aslprep/atlas-4S452Parcels_dseg.json -aslprep/atlas-4S452Parcels_dseg.tsv -aslprep/atlas-4S552Parcels_dseg.json -aslprep/atlas-4S552Parcels_dseg.tsv -aslprep/atlas-4S652Parcels_dseg.json -aslprep/atlas-4S652Parcels_dseg.tsv -aslprep/atlas-4S752Parcels_dseg.json -aslprep/atlas-4S752Parcels_dseg.tsv -aslprep/atlas-4S852Parcels_dseg.json -aslprep/atlas-4S852Parcels_dseg.tsv -aslprep/atlas-4S952Parcels_dseg.json -aslprep/atlas-4S952Parcels_dseg.tsv +aslprep/atlas-4S1056Parcels_dseg.json +aslprep/atlas-4S1056Parcels_dseg.tsv +aslprep/atlas-4S156Parcels_dseg.json +aslprep/atlas-4S156Parcels_dseg.tsv +aslprep/atlas-4S256Parcels_dseg.json +aslprep/atlas-4S256Parcels_dseg.tsv +aslprep/atlas-4S356Parcels_dseg.json +aslprep/atlas-4S356Parcels_dseg.tsv +aslprep/atlas-4S456Parcels_dseg.json +aslprep/atlas-4S456Parcels_dseg.tsv +aslprep/atlas-4S556Parcels_dseg.json +aslprep/atlas-4S556Parcels_dseg.tsv +aslprep/atlas-4S656Parcels_dseg.json +aslprep/atlas-4S656Parcels_dseg.tsv +aslprep/atlas-4S756Parcels_dseg.json +aslprep/atlas-4S756Parcels_dseg.tsv +aslprep/atlas-4S856Parcels_dseg.json +aslprep/atlas-4S856Parcels_dseg.tsv +aslprep/atlas-4S956Parcels_dseg.json +aslprep/atlas-4S956Parcels_dseg.tsv aslprep/atlas-Glasser_dseg.json aslprep/atlas-Glasser_dseg.tsv aslprep/atlas-Gordon_dseg.json @@ -32,26 +32,26 @@ aslprep/logs/CITATION.html aslprep/logs/CITATION.md aslprep/logs/CITATION.tex aslprep/qc.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S1052Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S152Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S152Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S252Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S252Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S352Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S352Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S452Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S452Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S552Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S552Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S652Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S652Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S752Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S752Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S852Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S852Parcels_res-01_dseg.nii.gz -aslprep/space-MNI152NLin6Asym_atlas-4S952Parcels_res-01_dseg.json -aslprep/space-MNI152NLin6Asym_atlas-4S952Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz +aslprep/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.json +aslprep/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.json aslprep/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz aslprep/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.json @@ -66,16 +66,16 @@ aslprep/sub-A00086748/ses-BAS1 aslprep/sub-A00086748/ses-BAS1/perf aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_aslref.json aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_aslref.nii.gz -aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S1052Parcels_cbf.tsv -aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S152Parcels_cbf.tsv -aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S252Parcels_cbf.tsv -aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S352Parcels_cbf.tsv -aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S452Parcels_cbf.tsv -aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S552Parcels_cbf.tsv -aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S652Parcels_cbf.tsv -aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S752Parcels_cbf.tsv -aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S852Parcels_cbf.tsv -aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S952Parcels_cbf.tsv +aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S1056Parcels_cbf.tsv +aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S156Parcels_cbf.tsv +aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S256Parcels_cbf.tsv +aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S356Parcels_cbf.tsv +aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S456Parcels_cbf.tsv +aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S556Parcels_cbf.tsv +aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S656Parcels_cbf.tsv +aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S756Parcels_cbf.tsv +aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S856Parcels_cbf.tsv +aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-4S956Parcels_cbf.tsv aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-Glasser_cbf.tsv aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-Gordon_cbf.tsv aslprep/sub-A00086748/ses-BAS1/perf/sub-A00086748_ses-BAS1_atlas-HCP_cbf.tsv diff --git a/aslprep/tests/run_local_tests.py b/aslprep/tests/run_local_tests.py index fc443e10e..3636df5e7 100644 --- a/aslprep/tests/run_local_tests.py +++ b/aslprep/tests/run_local_tests.py @@ -66,9 +66,9 @@ def run_command(command, env=None): def run_tests(test_regex, test_mark): """Run the tests.""" local_patch = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))) - mounted_code = "/usr/local/miniconda/lib/python3.8/site-packages/aslprep" + mounted_code = "/usr/local/miniconda/lib/python3.9/site-packages/aslprep" run_str = "docker run --rm -ti " - run_str += f"-v {local_patch}:/usr/local/miniconda/lib/python3.8/site-packages/aslprep " + run_str += f"-v {local_patch}:/usr/local/miniconda/lib/python3.9/site-packages/aslprep " run_str += "--entrypoint pytest " run_str += "pennlinc/aslprep:unstable " run_str += ( diff --git a/aslprep/utils/atlas.py b/aslprep/utils/atlas.py index fe1bd8acf..2ed6041ae 100644 --- a/aslprep/utils/atlas.py +++ b/aslprep/utils/atlas.py @@ -24,16 +24,16 @@ def get_atlas_names(subset): """ atlases = { "cortical": [ - "4S152Parcels", - "4S252Parcels", - "4S352Parcels", - "4S452Parcels", - "4S552Parcels", - "4S652Parcels", - "4S752Parcels", - "4S852Parcels", - "4S952Parcels", - "4S1052Parcels", + "4S156Parcels", + "4S256Parcels", + "4S356Parcels", + "4S456Parcels", + "4S556Parcels", + "4S656Parcels", + "4S756Parcels", + "4S856Parcels", + "4S956Parcels", + "4S1056Parcels", "Glasser", "Gordon", ], @@ -55,9 +55,9 @@ def get_atlas_nifti(atlas_name): Parameters ---------- - atlas_name : {"4S152Parcels", "4S252Parcels", "4S352Parcels", "4S452Parcels", \ - "4S552Parcels", "4S652Parcels", "4S752Parcels", "4S852Parcels", \ - "4S952Parcels", "4S1052Parcels", "Glasser", "Gordon", \ + atlas_name : {"4S156Parcels", "4S256Parcels", "4S356Parcels", "4S456Parcels", \ + "4S556Parcels", "4S656Parcels", "4S756Parcels", "4S856Parcels", \ + "4S956Parcels", "4S1056Parcels", "Glasser", "Gordon", \ "Tian", "HCP"} The name of the NIFTI atlas to fetch. @@ -112,9 +112,9 @@ def get_atlas_cifti(atlas_name): Parameters ---------- - atlas_name : {"4S152Parcels", "4S252Parcels", "4S352Parcels", "4S452Parcels", \ - "4S552Parcels", "4S652Parcels", "4S752Parcels", "4S852Parcels", \ - "4S952Parcels", "4S1052Parcels", "Glasser", "Gordon", \ + atlas_name : {"4S156Parcels", "4S256Parcels", "4S356Parcels", "4S456Parcels", \ + "4S556Parcels", "4S656Parcels", "4S756Parcels", "4S856Parcels", \ + "4S956Parcels", "4S1056Parcels", "Glasser", "Gordon", \ "Tian", "HCP"} The name of the CIFTI atlas to fetch. diff --git a/aslprep/utils/bids.py b/aslprep/utils/bids.py index 3227dccc3..399cb3f9a 100644 --- a/aslprep/utils/bids.py +++ b/aslprep/utils/bids.py @@ -90,9 +90,9 @@ def collect_run_data(layout, asl_file): if len(m0scan_candidates) > 1: config.loggers.workflow.warning( f"More than one M0 file found for {asl_file}. " - f"Using the first one ({m0scan_candidates[0]})" + f"Using the first one ({m0scan_candidates[0].path})" ) - run_data["m0scan"] = m0scan_candidates[0] + run_data["m0scan"] = m0scan_candidates[0].path else: run_data["m0scan"] = None diff --git a/aslprep/workflows/asl/cbf.py b/aslprep/workflows/asl/cbf.py index 245692e94..d668c94c1 100644 --- a/aslprep/workflows/asl/cbf.py +++ b/aslprep/workflows/asl/cbf.py @@ -927,9 +927,9 @@ def init_parcellate_cbf_wf( atlas_names : list of str A list of atlases used for parcellating the CBF results. The list of atlas names is generated by :func:`aslprep.utils.atlas.get_atlas_names`. - The atlases include: "Schaefer117", "Schaefer217", "Schaefer317", "Schaefer417", - "Schaefer517", "Schaefer617", "Schaefer717", "Schaefer817", "Schaefer917", - "Schaefer1017", "Glasser", "Gordon", and "subcortical" (Tian). + The atlases include: "4S156Parcels", "4S256Parcels", "4S356Parcels", "4S456Parcels", + "4S556Parcels", "4S656Parcels", "4S756Parcels", "4S856Parcels", "4S956Parcels", + "4S1056Parcels", "Glasser", "Gordon", "Tian", and "HCP". mean_cbf_parcellated : list of str mean_cbf_score_parcellated : Undefined or list of str Only defined if ``scorescrub`` is True. @@ -945,10 +945,11 @@ def init_parcellate_cbf_wf( workflow.__desc__ = f""" Parcellated CBF estimates were extracted for the following atlases: the Schaefer Supplemented with Subcortical Structures (4S) atlas -[@Schaefer_2017,@pauli2018high,@king2019functional,@najdenovska2018vivo] at 10 different -resolutions (152, 252, 352, 452, 552, 652, 752, 852, 952, and 1052 parcels), +[@Schaefer_2017,@pauli2018high,@king2019functional,@najdenovska2018vivo,@glasser2013minimal] at +10 different resolutions (156, 256, 356, 456, 556, 656, 756, 856, 956, and 1056 parcels), the Glasser atlas [@Glasser_2016], the Gordon atlas [@Gordon_2014], -the Tian subcortical atlas [@tian2020topographic], and the CIFTI subcortical atlas. +the Tian subcortical atlas [@tian2020topographic], and the HCP CIFTI subcortical atlas +[@glasser2013minimal]. In cases of partial coverage, either uncovered voxels (values of all zeros or NaNs) were ignored (when the parcel had >{min_coverage * 100}% coverage) or the whole parcel was set to zero (when the parcel had <{min_coverage * 100}% coverage). diff --git a/docs/outputs.rst b/docs/outputs.rst index 9650bc937..a64a276e8 100644 --- a/docs/outputs.rst +++ b/docs/outputs.rst @@ -174,7 +174,9 @@ The 4S atlas combines the Schaefer 2018 cortical atlas (version v0143) :footcite at 10 different resolutions (100, 200, 300, 400, 500, 600, 700, 800, 900, and 1000 parcels) with the CIT168 subcortical atlas :footcite:p:`pauli2018high`, the Diedrichson cerebellar atlas :footcite:p:`king2019functional`, -and the HCP thalamic atlas :footcite:p:`najdenovska2018vivo`. +the HCP thalamic atlas :footcite:p:`najdenovska2018vivo`, +and the amygdala and hippocampus parcels from the HCP CIFTI subcortical parcellation +:footcite:p:`glasser2013minimal`. The 4S atlas is used in the same manner across three PennLINC BIDS Apps: ASLPrep, QSIPrep_, and XCP-D, to produce synchronized outputs across modalities. For more information about the 4S atlas, please see https://github.com/PennLINC/AtlasPack.