Merge pull request #753 from mgxd/enh/path2bids-regex

ENH: Add morphometric suffixes to pattern matching
nipreps · Oct 18, 2022 · 5b898c4 · 5b898c4
2 parents e5fc210 + a46f5d9
commit 5b898c4
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/niworkflows/data/nipreps.json b/niworkflows/data/nipreps.json
@@ -154,7 +154,7 @@
   "default_path_patterns": [
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio|T2starw|MTw|TSE>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_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}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}]_{suffix<wm|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat>}{extension<.surf.gii>}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}]_{suffix<wm|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|sulc|curv|thickness>}{extension<.surf.gii|.shape.gii>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_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}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<bold|cbv|sbref|boldref|dseg>}{extension<.nii|.nii.gz|.json>|.nii.gz}",

diff --git a/niworkflows/interfaces/surf.py b/niworkflows/interfaces/surf.py
@@ -154,13 +154,19 @@ class Path2BIDS(SimpleInterface):
     suffix = smoothwm
     <BLANKLINE>
 
+    >>> Path2BIDS(in_file='lh.sulc_converted.gii').run().outputs
+    <BLANKLINE>
+    extension = .gii
+    hemi = L
+    suffix = sulc
+    <BLANKLINE>
     """
 
     input_spec = _Path2BIDSInputSpec
     output_spec = _Path2BIDSOutputSpec
     _pattern = re.compile(
         r"(?P<hemi>[lr])h.(?P<suffix>(wm|smoothwm|pial|midthickness|"
-        r"inflated|vinflated|sphere|flat))[\w\d_-]*(?P<extprefix>\.\w+)?"
+        r"inflated|vinflated|sphere|flat|sulc|curv|thickness))[\w\d_-]*(?P<extprefix>\.\w+)?"
     )
     _excluded = ("extprefix",)