add to init and changes, rename some arguments and add descriptions, add

example

Author: juhuntenburg

CHANGES

@@ -1,6 +1,7 @@
 Next Release
 ============
 
+* ENH: New Freesurfer interface: Tkregister2 (for conversion of fsl style matrices to freesurfer format)
 * ENH: New FSL interfaces: WarpPoints, WarpPointsToStd.
 * ENH: New Freesurfer interface: MRIPretess
 * ENH: New miscelaneous interface: AddCSVRow

nipype/interfaces/freesurfer/__init__.py

@@ -12,4 +12,4 @@
 from .utils import (SampleToSurface, SurfaceSmooth, SurfaceTransform, Surface2VolTransform,
                     SurfaceSnapshots,ApplyMask, MRIsConvert, MRITessellate, MRIPretess,
                     MRIMarchingCubes, SmoothTessellation, MakeAverageSubject,
-                    ExtractMainComponent)
+                    ExtractMainComponent, Tkregister2)

nipype/interfaces/freesurfer/utils.py

@@ -1189,22 +1189,39 @@ class ExtractMainComponent(CommandLine):
     input_spec=ExtractMainComponentInputSpec
     output_spec=ExtractMainComponentOutputSpec
 
-class Tkregister2InputSpec(FSTraitedSpec):
-
-    mov = File(exists=True, mandatory=True, argstr="--mov %s")
-    fsl = File(exists=True, argstr="--fsl %s")
-    subject_id = traits.String(argstr="--s %s", mandatory=True)
-    noedit = traits.Bool(argstr="--noedit")
-    out_reg_file = File(name_template='%s.dat', name_source='fsl', mandatory=True, argstr="--reg %s")
 
+class Tkregister2InputSpec(FSTraitedSpec):
+    moving_image = File(exists=True, mandatory=True, argstr="--mov %s", 
+               desc='moving volume')
+    fsl_in_matrix = File(exists=True, argstr="--fsl %s", 
+               desc='fsl-style registration input matrix')
+    subject_id = traits.String(argstr="--s %s", mandatory=True, 
+                               desc='freesurfer subject ID')
+    subjects_dir = traits.Str(argstr='--sd %s',
+                              desc=('freesurfer subjects directory defaults to $SUBJECTS_DIR'))
+    noedit = traits.Bool(True, argstr="--noedit", desc='do not open edit window (exit)', usedefault=True)
+    reg_file = File(name_template='%s.dat', name_source='fsl', 
+                        mandatory=True, argstr="--reg %s", 
+                        desc='freesurfer-style registration file')
 
 class Tkregister2OutputSpec(TraitedSpec):
+    reg_file = File(exists=True, desc='freesurfer-style registration file')
 
-    out_reg_file = File(exists=True)
+class Tkregister2(FSCommand):
+    """Use tkregister2 without the manual editing stage to convert 
+    FSL-style registration matrix (.mat) to FreeSurfer-style registration matrix (.dat)
 
+    Examples
+    --------
 
-class Tkregister2(FSCommand):
-    
+    >>> from nipype.interfaces.freesurfer import Tkregister2
+    >>> tk2 = Tkregister2(reg_file='register.dat')
+    >>> tk2.inputs.moving_image = 'func.nii.gz'
+    >>> tk2.inputs.fsl_in_matrix = 'func2anat.mat'
+    >>> tk2.inputs.subject_id = 'test_subject'
+    >>> tk2.inputs.subjects_dir = '.'
+    >>> tk2.run()
+    """
     _cmd = "tkregister2"
     input_spec = Tkregister2InputSpec
     output_spec = Tkregister2OutputSpec