Merge pull request #280 from agramfort/fix_coreg_mgh

MRG : coreg for MGH images + cosmits

Author: bthirion

pypreprocess/coreg.py

@@ -358,7 +358,7 @@ def fit(self, target, source):
         self.params_ = np.array(self.params_init)
         for samp in self.sep:
             print("\r\nRunning Powell gradient-less local optimization "
-                  "(pyramidal level = %smm)...") % samp
+                  "(pyramidal level = %smm)..." % samp)
 
             # create sampled grid for target img
             grid = make_sampled_grid(target.shape, samp=_correct_voxel_samp(
@@ -406,15 +406,15 @@ def transform(self, source, output_dir=None, prefix="", ext=".nii.gz",
             the coregistered source volume
         """
         # save output unto disk
-        if not output_dir is None:
+        if output_dir is not None:
             if basenames is None:
                 basenames = get_basenames(source)
 
         # apply coreg
         # XXX backend should handle nasty i/o logic!!
         coregistered_source = list(apply_realignment(source, self.params_,
                                                      inverse=True))
-        if not output_dir is None:
+        if output_dir is not None:
             concat = isinstance(basenames, _basestring)
             coregistered_source = save_vols(coregistered_source,
                                             output_dir=output_dir,

pypreprocess/io_utils.py

@@ -31,7 +31,8 @@ def is_niimg(img):
     if isinstance(img, (nibabel.Nifti1Image,
                         nibabel.Nifti1Pair,
                         nibabel.Spm2AnalyzeImage,
-                        nibabel.Spm99AnalyzeImage
+                        nibabel.Spm99AnalyzeImage,
+                        nibabel.MGHImage,
                         # add other supported image types below (e.g
                         # AnalyseImage, etc.)
                         )):