Merge pull request #426 from grlee77/parrec_v40

MRG: properly handle V4 .PAR files with diffusion info

This PR fixes a bug in `get_bvals_bvecs` for V4 .PAR files (the bug is only present for V4, not the more recent V4.1 or V4.2).  In V4, the `diffusion` field does not exist and the `bvecs` cannot be determined.

Author: matthew-brett

bin/parrec2nii

@@ -185,7 +185,7 @@ def proc_file(infile, opts):
 
     bvals, bvecs = pr_hdr.get_bvals_bvecs()
     if not opts.keep_trace:  # discard Philips DTI trace if present
-        if bvals is not None:
+        if bvecs is not None:
             bad_mask = np.logical_and(bvals != 0, (bvecs == 0).all(axis=1))
             if bad_mask.sum() > 0:
                 pl = 's' if bad_mask.sum() != 1 else ''
@@ -229,6 +229,14 @@ def proc_file(infile, opts):
     if opts.bvs:
         if bvals is None and bvecs is None:
             verbose('No DTI volumes detected, bvals and bvecs not written')
+        elif bvecs is None:
+            verbose('DTI volumes detected, but no diffusion direction info was'
+                    'found.  Writing .bvals file only.')
+            with open(basefilename + '.bvals', 'w') as fid:
+                # np.savetxt could do this, but it's just a loop anyway
+                for val in bvals:
+                    fid.write('%s ' % val)
+                fid.write('\n')
         else:
             verbose('Writing .bvals and .bvecs files')
             # Transform bvecs with reorientation affine

nibabel/parrec.py

@@ -703,7 +703,7 @@ def get_q_vectors(self):
             acquisition.
         """
         bvals, bvecs = self.get_bvals_bvecs()
-        if bvals is None and bvecs is None:
+        if bvals is None or bvecs is None:
             return None
         return bvecs * bvals[:, np.newaxis]
 
@@ -728,6 +728,8 @@ def get_bvals_bvecs(self):
         # All bvals within volume should be the same
         assert not np.any(np.diff(bvals, axis=0))
         bvals = bvals[0]
+        if 'diffusion' not in self.image_defs.dtype.names:
+            return bvals, None
         bvecs = self.image_defs['diffusion'][reorder].reshape(
             (n_slices, n_vols, 3), order='F')
         # All 3 values of bvecs should be same within volume