fsl/data/freesurfer.py

@@ -67,7 +67,8 @@ CORE_GEOMETRY_FILES = ['?h.orig',
                        '?h.pial',
                        '?h.white',
                        '?h.inflated',
-                       '?h.sphere']
+                       '?h.sphere',
+                       '?h.pial_semi_inflated']
 """File patterns for identifying the core Freesurfer geometry files. """
 
 
@@ -76,7 +77,8 @@ CORE_GEOMETRY_DESCRIPTIONS = [
     "Freesurfer surface (pial)",
     "Freesurfer surface (white matter)",
     "Freesurfer surface (inflated)",
-    "Freesurfer surface (sphere)"]
+    "Freesurfer surface (sphere)",
+    "Freesurfer surface (pial semi-inflated)"]
 """A description for each extension in :attr:`GEOMETRY_EXTENSIONS`. """
 
 

fsl/data/melodicanalysis.py

@@ -33,7 +33,6 @@ import logging
 import os.path as op
 import numpy   as np
 
-import fsl.utils.path        as fslpath
 import fsl.data.image        as fslimage
 import fsl.data.featanalysis as featanalysis
 
@@ -63,10 +62,9 @@ def isMelodicImage(path):
 
 
 def isMelodicDir(path):
-    """Returns ``True`` if the given path looks like it is contained within
-    a MELODIC directory, ``False`` otherwise. A melodic directory:
+    """Returns ``True`` if the given path looks like it is a MELODIC directory,
+    ``False`` otherwise. A MELODIC directory:
 
-      - Must be named ``*.ica``.
       - Must contain a file called ``melodic_IC.nii.gz`` or
         ``melodic_oIC.nii.gz``.
       - Must contain a file called ``melodic_mix``.
@@ -75,12 +73,7 @@ def isMelodicDir(path):
 
     path = op.abspath(path)
 
-    if op.isdir(path): dirname = path
-    else:              dirname = op.dirname(path)
-
-    sufs = ['.ica']
-
-    if not any([dirname.endswith(suf) for suf in sufs]):
+    if not op.isdir(path):
         return False
 
     # Must contain an image file called
@@ -88,7 +81,7 @@ def isMelodicDir(path):
     prefixes = ['melodic_IC', 'melodic_oIC']
     for p in prefixes:
         try:
-            fslimage.addExt(op.join(dirname, p))
+            fslimage.addExt(op.join(path, p))
             break
         except fslimage.PathError:
             pass
@@ -97,8 +90,8 @@ def isMelodicDir(path):
 
     # Must contain files called
     # melodic_mix and melodic_FTmix
-    if not op.exists(op.join(dirname, 'melodic_mix')):   return False
-    if not op.exists(op.join(dirname, 'melodic_FTmix')): return False
+    if not op.exists(op.join(path, 'melodic_mix')):   return False
+    if not op.exists(op.join(path, 'melodic_FTmix')): return False
 
     return True
 
@@ -108,10 +101,13 @@ def getAnalysisDir(path):
     to that MELODIC directory is returned. Otherwise, ``None`` is returned.
     """
 
-    meldir = fslpath.deepest(path, ['.ica'])
+    if not op.isdir(path):
+        path = op.dirname(path)
 
-    if meldir is not None and isMelodicDir(meldir):
-        return meldir
+    while path not in (op.sep, ''):
+        if isMelodicDir(path):
+            return path
+        path = op.dirname(path)
 
     return None
 
@@ -137,10 +133,18 @@ def getDataFile(meldir):
     if topDir is None:
         return None
 
-    dataFile = op.join(topDir, 'filtered_func_data')
+    # People often rename filtered_func_data.nii.gz
+    # to something like filtered_func_data_clean.nii.gz,
+    # because that is the recommended approach when
+    # performing ICA-based denoising). So we try both.
+    candidates = ['filtered_func_data', 'filtered_func_data_clean']
 
-    try:                       return fslimage.addExt(dataFile)
-    except fslimage.PathError: return None
+    for candidate in candidates:
+        dataFile = op.join(topDir, candidate)
+        try:                       return fslimage.addExt(dataFile)
+        except fslimage.PathError: continue
+
+    return None
 
 
 def getMeanFile(meldir):
@@ -187,7 +191,7 @@ def getNumComponents(meldir):
     contained in the given directrory.
     """
 
-    icImg = fslimage.Image(getICFile(meldir), loadData=False, calcRange=False)
+    icImg = fslimage.Image(getICFile(meldir))
     return icImg.shape[3]