Enh/fsutils

CHANGES

@@ -1,6 +1,8 @@
 Release 0.3.4 (FUTURE)
 ======================
 
+* ENH: Added support for sampling a volume onto a FreeSurfer surface
+* ENH: Added support for saving pictures of FreeSurfer surfaces using tksurfer
 * ENH: Added support for flash processing using FreeSurfer
 
 * BF: Diffusion toolkit gets installed 

nipype/interfaces/freesurfer/__init__.py

@@ -14,4 +14,4 @@
 from nipype.interfaces.freesurfer.model import (MRISPreproc, GLMFit,
  OneSampleTTest, Binarize,
  Concatenate, SegStats, Label2Vol)
-
+from nipype.interfaces.freesurfer.utils import (SampleToSurface, SurfaceScreenshots)

nipype/interfaces/freesurfer/tests/test_utils.py

@@ -0,0 +1,126 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+import os
+from tempfile import mkdtemp
+from shutil import rmtree
+
+import numpy as np
+
+import nipype.externals.pynifti as nif
+from nipype.testing import (assert_equal, assert_not_equal,
+ assert_raises, parametric, skipif)
+from nipype.interfaces.base import TraitError
+
+import nipype.interfaces.freesurfer as fs
+
+def no_freesurfer():
+ if fs.Info().version is None:
+ return True
+ else:
+ return False
+
+def create_files_in_directory():
+ outdir = mkdtemp()
+ cwd = os.getcwd()
+ os.chdir(outdir)
+ filelist = ['a.nii','b.nii']
+ for f in filelist:
+ hdr = nif.Nifti1Header()
+ shape = (3,3,3,4)
+ hdr.set_data_shape(shape)
+ img = np.random.random(shape)
+ nif.save(nif.Nifti1Image(img,np.eye(4),hdr),
+ os.path.join(outdir,f))
+ return filelist, outdir, cwd
+
+def clean_directory(outdir, old_wd):
+ if os.path.exists(outdir):
+ rmtree(outdir)
+ os.chdir(old_wd)
+
+@skipif(no_freesurfer)
+def test_sample2surf():
+
+ s2s = fs.SampleToSurface()
+ # Test underlying command
+ yield assert_equal, s2s.cmd, 'mri_vol2surf'
+
+ # Test mandatory args exception
+ yield assert_raises, ValueError, s2s.run
+
+ # Create testing files
+ files, cwd, oldwd = create_files_in_directory()
+
+ # Test input settings
+ s2s.inputs.source_file = files[0]
+ s2s.inputs.reference_file = files[1]
+ s2s.inputs.hemi = "lh"
+ s2s.inputs.sampling_range = .5
+ s2s.inputs.sampling_units = "frac"
+ s2s.inputs.sampling_method = "point"
+
+ # Test a basic command line
+ yield assert_equal, s2s.cmdline, ("mri_vol2surf "
+ "--hemi lh --o %s --ref %s --projfrac 0.500 --mov %s"
+ %(os.path.join(cwd, "lh.a.mgz"),files[1],files[0]))
+
+ # Test identity
+ s2sish = fs.SampleToSurface(source_file = files[1], reference_file = files[0],hemi="rh")
+ yield assert_not_equal, s2s, s2sish
+
+ # Test hits file name creation
+ s2s.inputs.hits_file = True
+ yield assert_equal, s2s._get_outfilename("hits_file"), os.path.join(cwd, "lh.a_hits.mgz")
+
+ # Test that a 2-tuple range raises an error
+ def set_illegal_range():
+ s2s.inputs.sampling_range = (.2, .5)
+ yield assert_raises, TraitError, set_illegal_range
+
+ # Clean up our mess
+ clean_directory(cwd, oldwd)
+
+@skipif(no_freesurfer)
+def test_surfshots():
+
+ fotos = fs.SurfaceScreenshots()
+
+ # Test underlying command
+ yield assert_equal, fotos.cmd, "tksurfer"
+
+ # Test mandatory args exception
+ yield assert_raises, ValueError, fotos.run
+
+ # Create testing files
+ files, cwd, oldwd = create_files_in_directory()
+
+ # Test input settins
+ fotos.inputs.subject = "fsaverage"
+ fotos.inputs.hemi = "lh"
+ fotos.inputs.surface = "pial"
+
+ # Test a basic command line
+ yield assert_equal, fotos.cmdline, "tksurfer fsaverage lh pial -tcl screenshots.tcl"
+
+ # Test identity
+ schmotos = fs.SurfaceScreenshots(subject="mysubject",hemi="rh",surface="white")
+ yield assert_not_equal, fotos, schmotos
+
+ # Test that the tcl script gets written
+ fotos._write_tcl_script()
+ yield assert_equal, True, os.path.exists("screenshots.tcl") 
+
+ # Test that we can use a different tcl script
+ foo = open("other.tcl", "w").close()
+ fotos.inputs.tcl_script = "other.tcl"
+ yield assert_equal, fotos.cmdline, "tksurfer fsaverage lh pial -tcl other.tcl"
+
+ # Test that the interface crashes politely if graphics aren't enabled
+ hold_display = os.environ["DISPLAY"]
+ del os.environ["DISPLAY"]
+ yield assert_raises, RuntimeError, fotos.run
+ os.environ["DISPLAY"] = hold_display
+
+ # Clean up our mess
+ clean_directory(cwd, oldwd)