Merge remote-tracking branch 'upstream/master'

Author: Kesshi Jordan

.zenodo.json

@@ -523,6 +523,11 @@
       "affiliation": "University of Amsterdam",
       "name": "Lukas Snoek",
       "orcid": "0000-0001-8972-204X"
+    },
+    {
+      "affiliation": "Vrije Universiteit, Amsterdam",
+      "name": "Gilles de Hollander",
+      "orcid": "0000-0003-1988-5091"
     }
   ],
   "keywords": [

nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py

@@ -14,23 +14,27 @@ def test_LTAConvert_inputs():
     ),
     in_fsl=dict(argstr='--infsl %s',
     mandatory=True,
-    xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg'),
+    xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'),
+    ),
+    in_itk=dict(argstr='--initk %s',
+    mandatory=True,
+    xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'),
     ),
     in_lta=dict(argstr='--inlta %s',
     mandatory=True,
-    xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg'),
+    xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'),
     ),
     in_mni=dict(argstr='--inmni %s',
     mandatory=True,
-    xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg'),
+    xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'),
     ),
     in_niftyreg=dict(argstr='--inniftyreg %s',
     mandatory=True,
-    xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg'),
+    xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'),
     ),
     in_reg=dict(argstr='--inreg %s',
     mandatory=True,
-    xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg'),
+    xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'),
     ),
     invert=dict(argstr='--invert',
     ),
@@ -39,6 +43,8 @@ def test_LTAConvert_inputs():
     ),
     out_fsl=dict(argstr='--outfsl %s',
     ),
+    out_itk=dict(argstr='--outitk %s',
+    ),
     out_lta=dict(argstr='--outlta %s',
     ),
     out_mni=dict(argstr='--outmni %s',
@@ -63,6 +69,7 @@ def test_LTAConvert_inputs():
 
 def test_LTAConvert_outputs():
     output_map = dict(out_fsl=dict(),
+    out_itk=dict(),
     out_lta=dict(),
     out_mni=dict(),
     out_reg=dict(),

nipype/interfaces/freesurfer/utils.py

@@ -3084,7 +3084,7 @@ def _normalize_filenames(self):
 
 class LTAConvertInputSpec(CommandLineInputSpec):
     # Inputs
-    _in_xor = ('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg')
+    _in_xor = ('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk')
     in_lta = traits.Either(
         File(exists=True), 'identity.nofile', argstr='--inlta %s',
         mandatory=True, xor=_in_xor, desc='input transform of LTA type')
@@ -3100,6 +3100,9 @@ class LTAConvertInputSpec(CommandLineInputSpec):
     in_niftyreg = File(
         exists=True, argstr='--inniftyreg %s', mandatory=True, xor=_in_xor,
         desc='input transform of Nifty Reg type (inverse RAS2RAS)')
+    in_itk = File(
+        exists=True, argstr='--initk %s', mandatory=True, xor=_in_xor,
+        desc='input transform of ITK type')
     # Outputs
     out_lta = traits.Either(
         traits.Bool, File, argstr='--outlta %s',
@@ -3110,6 +3113,8 @@ class LTAConvertInputSpec(CommandLineInputSpec):
                             desc='output transform in MNI/XFM format')
     out_reg = traits.Either(traits.Bool, File, argstr='--outreg %s',
                             desc='output transform in reg dat format')
+    out_itk = traits.Either(traits.Bool, File, argstr='--outitk %s',
+                            desc='output transform in ITK format')
     # Optional flags
     invert = traits.Bool(argstr='--invert')
     ltavox2vox = traits.Bool(argstr='--ltavox2vox', requires=['out_lta'])
@@ -3124,6 +3129,7 @@ class LTAConvertOutputSpec(TraitedSpec):
     out_fsl = File(exists=True, desc='output transform in FSL format')
     out_mni = File(exists=True, desc='output transform in MNI/XFM format')
     out_reg = File(exists=True, desc='output transform in reg dat format')
+    out_itk = File(exists=True, desc='output transform in ITK format')
 
 
 class LTAConvert(CommandLine):
@@ -3146,7 +3152,8 @@ def _format_arg(self, name, spec, value):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         for name, default in (('out_lta', 'out.lta'), ('out_fsl', 'out.mat'),
-                              ('out_mni', 'out.xfm'), ('out_reg', 'out.dat')):
+                              ('out_mni', 'out.xfm'), ('out_reg', 'out.dat'),
+                              ('out_itk', 'out.txt')):
             attr = getattr(self.inputs, name)
             if attr:
                 fname = default if attr is True else attr