enh: added new options to apply volume transform

Author: satra

nipype/interfaces/freesurfer/preprocess.py

@@ -784,6 +784,8 @@ class ApplyVolTransformInputSpec(FSTraitedSpec):
                       desc='Output template volume', mandatory=True)
     tal = traits.Bool(argstr='--tal', xor=_targ_xor, mandatory=True,
                       desc='map to a sub FOV of MNI305 (with --reg only)')
+    tal_resolution = traits.Float(argstr="--talres %.10f",
+                                  desc="Resolution to sample when using tal")
     fs_target = traits.Bool(argstr='--fstarg', xor=_targ_xor, mandatory=True,
                          requires=['reg_file'],
                          desc='use orig.mgz from subject in regfile as target')
@@ -805,10 +807,30 @@ class ApplyVolTransformInputSpec(FSTraitedSpec):
                    desc='set matrix = identity and use subject for any templates')
     inverse = traits.Bool(desc='sample from target to source',
                           argstr='--inv')
-    interp = traits.Enum('trilin', 'nearest', argstr='--interp %s',
+    interp = traits.Enum('trilin', 'nearest', 'cubic', argstr='--interp %s',
                          desc='Interpolation method (<trilin> or nearest)')
     no_resample = traits.Bool(desc='Do not resample; just change vox2ras matrix',
                               argstr='--no-resample')
+    m3z_file = File(argstr="--m3z %s",
+                    desc=('This is the morph to be applied to the volume. '
+                          'Unless the morph is in mri/transforms (eg.: for '
+                          'talairach.m3z computed by reconall), you will need '
+                          'to specify the full path to this morph and use the '
+                          '--noDefM3zPath flag.'))
+    no_ded_m3z_path = traits.Bool(argstr="--noDefM3zPath",
+                                  requires=['m3z_file'],
+                                  desc=('To be used with the m3z flag. '
+                                        'Instructs the code not to look for the'
+                                        'm3z morph in the default location '
+                                        '(SUBJECTS_DIR/subj/mri/transforms), '
+                                        'but instead just use the path '
+                                        'indicated in --m3z.'))
+
+    invert_morph = traits.Bool(argstr="--inv-morph",
+                               requires=['m3z_file'],
+                               desc=('Compute and use the inverse of the '
+                                     'non-linear morph to resample the input '
+                                     'volume. To be used by --m3z.'))
 
 
 class ApplyVolTransformOutputSpec(TraitedSpec):
@@ -853,7 +875,7 @@ def _get_outfile(self):
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
-        outputs['transformed_file'] = self._get_outfile()
+        outputs['transformed_file'] = os.path.abspath(self._get_outfile())
         return outputs
 
     def _gen_filename(self, name):
@@ -1192,11 +1214,3 @@ def _gen_filename(self, name):
         if name == "out_file":
             return self._list_outputs()["out_file"]
         return None
-
-'''
-interfaces to do:
-
-mri_vol2surf
-mri_surf2vol
-mri_surf2surf
-'''