ENH: Add more registration options to mri_vol2vol

Author: effigies

nipype/interfaces/freesurfer/preprocess.py

@@ -1277,7 +1277,15 @@ class ApplyVolTransformInputSpec(FSTraitedSpec):
     fs_target = traits.Bool(argstr='--fstarg', xor=_targ_xor, mandatory=True,
                             requires=['reg_file'],
                             desc='use orig.mgz from subject in regfile as target')
-    _reg_xor = ('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject')
+    _reg_xor = ('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file',
+                'reg_header', 'mni_152_reg', 'subject')
+    reg_file = File(exists=True, xor=_reg_xor, argstr='--reg %s',
+                    mandatory=True,
+                    desc='tkRAS-to-tkRAS matrix   (tkregister2 format)')
+    lta_file = File(exists=True, xor=_reg_xor, argstr='--lta %s',
+                    mandatory=True, desc='Linear Transform Array file')
+    lta_inv_file = File(exists=True, xor=_reg_xor, argstr='--lta-inv %s',
+                        mandatory=True, desc='LTA, invert')
     reg_file = File(exists=True, xor=_reg_xor, argstr='--reg %s',
                     mandatory=True,
                     desc='tkRAS-to-tkRAS matrix   (tkregister2 format)')
@@ -1290,8 +1298,9 @@ class ApplyVolTransformInputSpec(FSTraitedSpec):
     reg_header = traits.Bool(xor=_reg_xor, argstr='--regheader',
                              mandatory=True,
                              desc='ScannerRAS-to-ScannerRAS matrix = identity')
-    subject = traits.Str(xor=_reg_xor, argstr='--s %s',
-                         mandatory=True,
+    mni_152_reg = traits.Bool(xor=_reg_xor, argstr='--regheader', mandatory=True,
+                              desc='target MNI152 space')
+    subject = traits.Str(xor=_reg_xor, argstr='--s %s', mandatory=True,
                          desc='set matrix = identity and use subject for any templates')
     inverse = traits.Bool(desc='sample from target to source',
                           argstr='--inv')

nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py

@@ -16,7 +16,7 @@ def test_ApplyVolTransform_inputs():
     ),
     fsl_reg_file=dict(argstr='--fsl %s',
     mandatory=True,
-    xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'),
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
@@ -28,28 +28,40 @@ def test_ApplyVolTransform_inputs():
     invert_morph=dict(argstr='--inv-morph',
     requires=['m3z_file'],
     ),
+    lta_file=dict(argstr='--lta %s',
+    mandatory=True,
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
+    ),
+    lta_inv_file=dict(argstr='--lta-inv %s',
+    mandatory=True,
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
+    ),
     m3z_file=dict(argstr='--m3z %s',
     ),
+    mni_152_reg=dict(argstr='--regheader',
+    mandatory=True,
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
+    ),
     no_ded_m3z_path=dict(argstr='--noDefM3zPath',
     requires=['m3z_file'],
     ),
     no_resample=dict(argstr='--no-resample',
     ),
     reg_file=dict(argstr='--reg %s',
     mandatory=True,
-    xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'),
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
     ),
     reg_header=dict(argstr='--regheader',
     mandatory=True,
-    xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'),
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
     ),
     source_file=dict(argstr='--mov %s',
     copyfile=False,
     mandatory=True,
     ),
     subject=dict(argstr='--s %s',
     mandatory=True,
-    xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'),
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
     ),
     subjects_dir=dict(),
     tal=dict(argstr='--tal',
@@ -69,7 +81,7 @@ def test_ApplyVolTransform_inputs():
     ),
     xfm_reg_file=dict(argstr='--xfm %s',
     mandatory=True,
-    xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'),
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
     ),
     )
     inputs = ApplyVolTransform.input_spec()