Freesurfer checks label and stats directories for vertex data

files. Adjustment to gifti.relatedFiles.

fsl/data/freesurfer.py

@@ -93,7 +93,6 @@ VERTEX_DATA_FILES = ['?h.thickness',
                      '?h.curv',
                      '?h.area',
                      '?h.sulc',
-                     '?h.*.stats',
                      '.mgh',
                      '.mgz']
 """File patterns which are interpreted as Freesurfer vertex data files,
@@ -225,7 +224,7 @@ class FreesurferMesh(fslmesh.Mesh):
 
         self.addVertexData(key, vdata)
 
-        if isvlabel:
+        if isvannot:
             self.__luts[key] = lut, names, lut
 
         return vdata
@@ -368,9 +367,20 @@ def relatedVertexDataFiles(fname):
     fpats   = VERTEX_DATA_FILES + VERTEX_LABEL_FILES + VERTEX_ANNOT_FILES
     fpats   = [hemi + p[1:] if p.startswith('?h') else p for p in fpats]
 
-    related = [glob.glob(op.join(dirname, p)) for p in fpats]
+    basedir    = op.dirname(dirname)
+    searchDirs = set([dirname,
+                      op.join(basedir, 'surf'),
+                      op.join(basedir, 'stats'),
+                      op.join(basedir, 'label')])
+
+    searchPats = it.product(searchDirs, fpats)
+
+    related = []
+
+    for sdir, spat in searchPats:
+        related.extend(glob.glob(op.join(sdir, spat)))
 
-    return list(it.chain(*related))
+    return related
 
 
 def findReferenceImage(fname):

fsl/data/gifti.py

@@ -77,6 +77,7 @@ class GiftiMesh(fslmesh.Mesh):
 
         surfimg, vertices, indices = loadGiftiMesh(infile)
 
+
         fslmesh.Mesh.__init__(self,
                               indices,
                               name=name,
@@ -278,35 +279,35 @@ def relatedFiles(fname, ftypes=None):
     # directory which have the following name:
 
     #
-    # [prefix].*[ftype]
+    # [subj].[hemi].[type].*.[ftype]
     #
+
     #   where
-    #     - prefix is the file prefix, and which
-    #       may include periods.
+    #     - [subj] is the subject ID, and matches fname
     #
-    #     - we don't care about the middle
+    #     - [hemi] is the hemisphere, and matches fname
     #
-    #     - suffix is func, shape, label, time, or `ftype`
+    #     - [type] defines the file contents
     #
+    #     - suffix is func, shape, label, time, or `ftype`
 
-    # We determine the unique prefix of the
-    # given file, and back-up to the most
-    # recent period. Then search for other
-    # files which have that same (non-unique)
-    # prefix.
-    prefix  = fslpath.uniquePrefix(fname)
-    lastdot = prefix.rfind('.')
-    prefix  = prefix[:lastdot]
+    path            = op.abspath(fname)
+    dirname, fname  = op.split(path)
 
-    if lastdot == -1:
+    # get the [subj].[hemi] prefix
+    try:
+        subj, hemi, _ = fname.split('.', 2)
+        prefix        = '.'.join((subj, hemi))
+    except Exception:
         return []
 
     related = []
 
     for ftype in ftypes:
-        related += list(glob.glob('{}*{}'.format(prefix, ftype)))
+        related.extend(
+            glob.glob(op.join(dirname, '{}*{}'.format(prefix, ftype))))
 
-    return [r for r in related if r != fname]
+    return [r for r in related if r != path]
 
 
 class GiftiSurface(fslmesh.TriangleMesh):