Merge pull request #420 from bpinsard/fix/dseg_tsv_copyany

[FIX] Require recent templateflow, select correct aparc dseg.tsv

Author: effigies

pyproject.toml

@@ -30,7 +30,7 @@ dependencies = [
     "packaging",
     "pybids >= 0.11.1",
     "pyyaml",
-    "templateflow >= 0.6",
+    "templateflow >= 24.1",
 ]
 dynamic = ["version"]
 

requirements.txt

@@ -188,7 +188,7 @@ sqlalchemy==2.0.28
     # via pybids
 svgutils==0.3.4
     # via niworkflows
-templateflow==24.0.0
+templateflow==24.2.0
     # via niworkflows
 threadpoolctl==3.3.0
     # via scikit-learn

smriprep/cli/run.py

@@ -413,7 +413,16 @@ def _warn_redirect(message, category, filename, lineno, file=None, line=None):
             from niworkflows.utils.misc import _copy_any
             from templateflow import api
 
-            dseg_tsv = str(api.get('fsaverage', suffix='dseg', extension=['.tsv']))
+            dseg_tsv = str(
+                api.get(
+                    'fsaverage',
+                    hemi=None,
+                    atlas=None,
+                    segmentation='aparc',
+                    suffix='dseg',
+                    extension=['.tsv'],
+                )
+            )
             _copy_any(dseg_tsv, str(Path(output_dir) / 'smriprep' / 'desc-aseg_dseg.tsv'))
             _copy_any(dseg_tsv, str(Path(output_dir) / 'smriprep' / 'desc-aparcaseg_dseg.tsv'))
         logger.log(25, 'sMRIPrep finished without errors')