Merge branch 'fix/mnibias' of github.com:mgxd/nipype into fix/mnibias

Author: mgxd

nipype/interfaces/freesurfer/preprocess.py

@@ -1510,6 +1510,7 @@ class MNIBiasCorrection(FSCommand):
     >>> from nipype.interfaces.freesurfer import MNIBiasCorrection
     >>> correct = MNIBiasCorrection()
     >>> correct.inputs.in_file = "norm.mgz"
+    >>> correct.inputs.out_file = "norm_output.mgz"
     >>> correct.inputs.iterations = 6
     >>> correct.inputs.protocol_iterations = 1000
     >>> correct.inputs.distance = 50

nipype/interfaces/freesurfer/tests/test_preprocess.py

@@ -102,11 +102,11 @@ def test_mandatory_outvol(create_files_in_directory):
     with pytest.raises(ValueError): mni.run()
 
     # rest of mandatory inputs
-    mni.inputs.out_file = 'bias_corrected_file'
+    mni.inputs.out_file = 'bias_corrected_output'
 
-    assert mni.cmdline == ('mri_nu_correct.mni --i %s --n 4 --o bias_corrected_file.mgz'
+    assert mni.cmdline == ('mri_nu_correct.mni --i %s --n 4 --o bias_corrected_output.mgz'
                             % filelist[0])
     # constructor based tests
-    mni2 = freesurfer.MNIBiasCorrection(in_file=filelist[0], out_file='bias_corrected_file')
-    assert mni2.cmdline == ('mri_nu_correct.mni --i %s --n 4 --o bias_corrected_file.mgz'
+    mni2 = freesurfer.MNIBiasCorrection(in_file=filelist[0], out_file='bias_corrected_output')
+    assert mni2.cmdline == ('mri_nu_correct.mni --i %s --n 4 --o bias_corrected_output.mgz'
                              % filelist[0])

nipype/interfaces/mrtrix/convert.py

@@ -10,7 +10,7 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import open
+from io import open
 
 import os.path as op
 import nibabel as nb
@@ -55,10 +55,11 @@ def read_mrtrix_tracks(in_file, as_generator=True):
 
 
 def read_mrtrix_header(in_file):
-    fileobj = open(in_file, 'r')
+    fileobj = open(in_file, 'rb')
     header = {}
     iflogger.info('Reading header data...')
     for line in fileobj:
+        line = line.decode()
         if line == 'END\n':
             iflogger.info('Reached the end of the header!')
             break
@@ -78,7 +79,7 @@ def read_mrtrix_header(in_file):
 def read_mrtrix_streamlines(in_file, header, as_generator=True):
     offset = header['offset']
     stream_count = header['count']
-    fileobj = open(in_file, 'r')
+    fileobj = open(in_file, 'rb')
     fileobj.seek(offset)
     endianness = native_code
     f4dt = np.dtype(endianness + 'f4')
@@ -90,7 +91,7 @@ def points_per_track(offset):
         n_points = 0
         track_points = []
         iflogger.info('Identifying the number of points per tract...')
-        all_str = fileobj.read()
+        all_str = fileobj.read().decode()
         num_triplets = int(len(all_str) / bytesize)
         pts = np.ndarray(shape=(num_triplets, pt_cols), dtype='f4', buffer=all_str)
         nonfinite_list = np.where(np.isfinite(pts[:, 2]) == False)