Merge pull request #382 from bpinsard/fix/io_spec

add missing fsLR reg sphere to io_spec
nipreps · Nov 9, 2023 · 2019064 · 2019064
2 parents 97a4098 + 7a20c4b
commit 2019064
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/smriprep/data/io_spec.json b/smriprep/data/io_spec.json
@@ -83,13 +83,21 @@
         "desc": "ribbon",
         "suffix": "mask",
         "extension": "nii.gz"
+      },
+      "sphere_reg_fsLR": {
+        "datatype" : "anat",
+        "hemi": ["L", "R"],
+        "space": "fsLR",
+        "desc": "reg",
+        "suffix": "sphere",
+        "extension": "surf.gii"
       }
     }
   },
   "patterns": [
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|dseg|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}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5>}",
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_hemi-{hemi<L|R>}_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|thickness|sulc|curv>}.{extension<surf.gii|shape.gii>}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_hemi-{hemi<L|R>}[_space-{space}][_desc-{desc}]_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|thickness|sulc|curv>}.{extension<surf.gii|shape.gii>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}]_desc-{desc}_{suffix<mask>|mask}.{extension<nii|nii.gz|json>|nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_space-{space}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}.{extension<nii|nii.gz|json>|nii.gz}"
   ]

diff --git a/smriprep/utils/bids.py b/smriprep/utils/bids.py
@@ -40,7 +40,7 @@ def get_outputnode_spec():
     'anat2std_xfm', 'std2anat_xfm',
     't1w_aseg', 't1w_aparc',
     't1w2fsnative_xfm', 'fsnative2t1w_xfm',
-    'surfaces', 'morphometrics', 'anat_ribbon']
+    'surfaces', 'morphometrics', 'anat_ribbon', 'sphere_reg_fsLR']
 
     """
     spec = loads(Path(pkgrf("smriprep", "data/io_spec.json")).read_text())["queries"]