From 0431b85c153325adff2491c486a9cf32f6d809c8 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 21 Jan 2018 18:45:07 +0000
Subject: [PATCH] Additions to freesurfer module - can now load vertex data.
---
fsl/data/freesurfer.py | 56 ++++++++++++++++++++++++++++++++++--------
1 file changed, 46 insertions(+), 10 deletions(-)
diff --git a/fsl/data/freesurfer.py b/fsl/data/freesurfer.py
index a8856334f..029274eab 100644
--- a/fsl/data/freesurfer.py
+++ b/fsl/data/freesurfer.py
@@ -20,10 +20,11 @@ The following functions are also available:
import os.path as op
import glob
-import nibabel as nib
+import nibabel.freesurfer as nibfs
-import fsl.utils.path as fslpath
-import fsl.data.mesh as fslmesh
+import fsl.utils.path as fslpath
+import fsl.data.mghimage as fslmgh
+import fsl.data.mesh as fslmesh
GEOMETRY_EXTENSIONS = ['.pial',
@@ -45,8 +46,14 @@ EXTENSION_DESCRIPTIONS = [
"""A description for each extension in :attr:`GEOMETRY_EXTENSIONS`. """
-
-VERTEX_DATA_EXTENSIONS = ['']
+VERTEX_DATA_EXTENSIONS = ['.curv',
+ '.crv',
+ '.area',
+ '.thickness',
+ '.volume',
+ '.mgh',
+ '.mgz']
+"""File extensions which are interpreted as Freesurfer vertex data files. """
class FreesurferMesh(fslmesh.Mesh):
@@ -68,7 +75,7 @@ class FreesurferMesh(fslmesh.Mesh):
loaded as additional vertex sets.
"""
- vertices, indices, meta, comment = nib.freesurfer.read_geometry(
+ vertices, indices, meta, comment = nibfs.read_geometry(
filename,
read_metadata=True,
read_stamp=True)
@@ -93,18 +100,47 @@ class FreesurferMesh(fslmesh.Mesh):
allFiles = relatedFiles(filename, ftypes=GEOMETRY_EXTENSIONS)
for f in allFiles:
- verts, idxs = nib.freesurfer.read_geometry(f)
+ verts, idxs = nibfs.read_geometry(f)
self.addVertices(verts, f, select=False)
def loadVertexData(self, infile, key=None):
+ """Overrides :meth:`.Mesh.loadVertexData`. If the given ``infile``
+ looks like a Freesurfer file, it is loaded via the
+ :func:`loadFreesurferVertexFile` function. Otherwise, it is passed
+ through to the base-class function.
"""
- """
- pass
+
+ if not fslpath.hasExt(infile, VERTEX_DATA_EXTENSIONS):
+ return fslmesh.loadVertexData(infile, key)
+
+ infile = op.abspath(infile)
+
+ if key is None:
+ key = infile
+
+ vdata = loadFreesurferVertexFile(infile)
+
+ self.addVertexData(key, vdata)
+
+ return vdata
def loadFreesurferVertexFile(infile):
- pass
+ """Loads the given Freesurfer file, assumed to contain vertex-wise data.
+ """
+
+ # morphometry file
+ morphexts = ['.curv', '.crv', '.area', '.thickness', '.volume']
+
+ if fslpath.hasExt(infile, morphexts):
+ vdata = nibfs.read_morph_data(infile)
+
+ # MGH image file
+ elif fslpath.hasExt(infile, fslmgh.ALLOWED_EXTENSIONS):
+ vdata = fslmgh.MGHImage(infile)[:].squeeze()
+
+ return vdata
def relatedFiles(fname, ftypes=None):
--
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