Merge pull request #806 from effigies/fix/smoothwm-to-white

FIX: Move from smoothwm to white

Author: effigies

niworkflows/anat/freesurfer.py

@@ -44,7 +44,7 @@ def init_gifti_surface_wf(
     This workflow prepares GIFTI surfaces from a FreeSurfer subjects directory
     If midthickness (or graymid) surfaces do not exist, they are generated and
     saved to the subject directory as ``lh/rh.midthickness``.
-    These, along with the gray/white matter boundary (``lh/rh.smoothwm``), pial
+    These, along with the gray/white matter boundary (``lh/rh.white``), pial
     surfaces (``lh/rh.pial``) and inflated surfaces (``lh/rh.inflated``) are
     converted to GIFTI files.
     Additionally, the vertex coordinates are :py:class:`recentered
@@ -137,11 +137,11 @@ def init_gifti_surface_wf(
         (inputnode, fsnative_2_t1_xfm, [("in_t1w", "target_file")]),
         (fssource, fsnative_2_t1_xfm, [("orig", "source_file")]),
         # Generate midthickness surfaces and save to FreeSurfer derivatives
-        (fssource, midthickness, [("smoothwm", "in_file"), ("graymid", "graymid")]),
+        (fssource, midthickness, [("white", "in_file"), ("graymid", "graymid")]),
         (midthickness, save_midthickness, [("out_file", "surf.@graymid")]),
         # Produce valid GIFTI surface files (dense mesh)
         (fssource, surface_list, [
-            ("smoothwm", "in1"), ("pial", "in2"), ("inflated", "in3"),
+            ("white", "in1"), ("pial", "in2"), ("inflated", "in3"),
         ]),
         (save_midthickness, surface_list, [("out_file", "in4")]),
         (surface_list, fs_2_gii, [("out", "in_file")]),

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|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}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}]_{suffix<white|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}][_den-{density}]_{suffix<sulc|curv|thickness>}{extension<.dscalar.nii|.json>}",
     "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}",

niworkflows/interfaces/surf.py

@@ -48,6 +48,7 @@
 
 SECONDARY_ANAT_STRUC = {
     "smoothwm": "GrayWhite",
+    "white": "GrayWhite",
     "pial": "Pial",
     "midthickness": "GrayMid",
 }
@@ -165,7 +166,7 @@ class Path2BIDS(SimpleInterface):
     input_spec = _Path2BIDSInputSpec
     output_spec = _Path2BIDSOutputSpec
     _pattern = re.compile(
-        r"(?P<hemi>[lr])h.(?P<suffix>(wm|smoothwm|pial|midthickness|"
+        r"(?P<hemi>[lr])h.(?P<suffix>(white|smoothwm|pial|midthickness|"
         r"inflated|vinflated|sphere|flat|sulc|curv|thickness))[\w\d_-]*(?P<extprefix>\.\w+)?"
     )
     _excluded = ("extprefix",)