Merge branch 'main' into t2-coreg

PennLINC · Jul 1, 2024 · e3e55a4 · e3e55a4
2 parents bbed28b + f3c0bc4
commit e3e55a4
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diff --git a/.versions.json b/.versions.json
@@ -9,6 +9,8 @@
 		"0.2.6": "Ordering of probseg maps was incorrect.",
 		"0.2.7": "Ordering of probseg maps was incorrect.",
 		"0.2.8": "Ordering of probseg maps was incorrect.",
-		"0.7.0": "Broken entrypoint for Docker/Apptainer."
+		"0.6.0": "GIFTI outputs not separated by hemisphere.",
+		"0.7.0": "Broken entrypoint for Docker/Apptainer. GIFTI outputs not separated by hemisphere.",
+		"0.7.1": "GIFTI outputs not separated by hemisphere."
 	}
 }
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,25 @@
+## 0.7.2
+
+A patch release to fix GIFTI outputs.
+
+### 🐛 Bug Fixes
+
+* Split giftis by hemisphere by @tsalo in https://github.com/PennLINC/aslprep/pull/419
+
+**Full Changelog**: https://github.com/PennLINC/aslprep/compare/0.7.1...0.7.2
+
+
+## 0.7.1
+
+A hotfix release following 0.7.0.
+
+### 🐛 Bug Fixes
+
+* Fix the entrypoint path in the Dockerfile by @tsalo in https://github.com/PennLINC/aslprep/pull/413
+
+**Full Changelog**: https://github.com/PennLINC/aslprep/compare/0.7.0...0.7.1
+
+
 ## 0.7.0
 
 ### 🛠 Breaking Changes

diff --git a/CITATION.cff b/CITATION.cff
@@ -124,5 +124,5 @@ keywords:
   - BIDS-App
   - Neuroimaging
 license: BSD-3-Clause
-version: 0.7.0
-date-released: '2024-05-09'
+version: 0.7.2
+date-released: '2024-06-03'
diff --git a/aslprep/data/aslprep_bids_config.json b/aslprep/data/aslprep_bids_config.json
@@ -38,7 +38,8 @@
     "sub-{subject}[/ses-{session}]/{datatype<func|perf>|func}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<regressors|timeseries>|timeseries}{extension<.json|.tsv|.csv|>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_desc-{desc}]_{suffix<confounds>}{extension<.tsv|.json>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|att|cbf|coverage|mask>}{extension<.nii|.nii.gz|.json|.csv|.tsv>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_den-{den}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|att|cbf>}{extension<.dtseries.nii|.dscalar.nii|.json|.dscalar.json|.dtseries.json|.func.gii|.func.json>|.dtseries.nii}",
+    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_den-{den}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|att|cbf>}{extension<.dtseries.nii|.dscalar.nii|.json|.dscalar.json|.dtseries.json>|.dtseries.nii}",
+    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_hemi-{hemi<L|R>}][_space-{space}][_res-{res}][_den-{den}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|att|cbf>}{extension<json|.func.gii>|.func.gii}",
     "sub-{subject}[/ses-{session}]/{datatype<figures>|figures}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_res-{res}][_den-{den}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|att|cbf|basil|score|scrub|pvc|mask>}{extension<.svg|.png|.html>|.svg}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",

diff --git a/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_philips.txt b/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_philips.txt
@@ -232,21 +232,39 @@ sub-01/ses-philips2d/perf/sub-01_ses-philips2d_from-aslref_to-T1w_mode-image_xfm
 sub-01/ses-philips2d/perf/sub-01_ses-philips2d_from-aslref_to-T1w_mode-image_xfm.txt
 sub-01/ses-philips2d/perf/sub-01_ses-philips2d_from-orig_to-aslref_mode-image_xfm.json
 sub-01/ses-philips2d/perf/sub-01_ses-philips2d_from-orig_to-aslref_mode-image_xfm.txt
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_cbf.func.gii
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_cbf.json
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-basilGM_cbf.func.gii
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-basilGM_cbf.json
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-basilWM_cbf.func.gii
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-basilWM_cbf.json
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-basil_att.func.gii
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-basil_att.json
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-basil_cbf.func.gii
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-basil_cbf.json
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-scoreTimeseries_cbf.func.gii
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-scoreTimeseries_cbf.json
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-score_cbf.func.gii
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-score_cbf.json
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-scrub_cbf.func.gii
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-scrub_cbf.json
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-timeseries_cbf.func.gii
-sub-01/ses-philips2d/perf/sub-01_ses-philips2d_space-fsaverage5_desc-timeseries_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-basilGM_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-basilGM_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-basilWM_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-basilWM_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-basil_att.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-basil_att.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-basil_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-basil_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-scoreTimeseries_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-scoreTimeseries_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-score_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-score_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-scrub_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-scrub_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-timeseries_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-L_space-fsaverage5_desc-timeseries_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-basilGM_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-basilGM_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-basilWM_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-basilWM_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-basil_att.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-basil_att.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-basil_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-basil_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-scoreTimeseries_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-scoreTimeseries_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-score_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-score_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-scrub_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-scrub_cbf.json
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-timeseries_cbf.func.gii
+sub-01/ses-philips2d/perf/sub-01_ses-philips2d_hemi-R_space-fsaverage5_desc-timeseries_cbf.json
diff --git a/pyproject.toml b/pyproject.toml
@@ -18,24 +18,24 @@ license = {file = "LICENSE.md"}
 requires-python = ">=3.11"
 dependencies = [
     'importlib_resources; python_version < "3.12"',
-    "fmriprep @ git+https://github.com/nipreps/fmriprep.git@master",
+    "fmriprep ~= 24.0",
     "indexed_gzip <= 1.8.7",
     "looseversion",
     "networkx ~= 3.3",  # nipype needs networkx, but 3+ isn"t compatible with nipype 1.8.5
     "nibabel <= 5.2.1",
     "nilearn ~= 0.10.3",
     "nipype >= 1.8.5",
-    "nitransforms @ git+https://github.com/nipreps/niworkflows.git@master",
+    "nitransforms >= 21.0.0",
     "niworkflows ~= 1.10.0",
     "numpy >= 1.26",
     "packaging",
     "pandas",
     "psutil <= 5.9.8",
-    "pybids <= 0.16.4",
+    "pybids <= 0.16.5",
     "requests",
-    "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master",
-    "sentry-sdk <= 2.2.0",
-    "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
+    "sdcflows <= 2.8.1",
+    "sentry-sdk <= 2.7.1",
+    "smriprep <= 0.15",
     "templateflow <= 24.2.0",
     "toml",