Merge pull request #912 from juhuntenburg/enh/tkregister2

Enh/tkregister2

Author: oesteban

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/tests/test_auto_Tkregister2.py

@@ -0,0 +1,49 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.freesurfer.utils import Tkregister2
+
+def test_Tkregister2_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    fsl_in_matrix=dict(argstr='--fsl %s',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    moving_image=dict(argstr='--mov %s',
+    mandatory=True,
+    ),
+    noedit=dict(argstr='--noedit',
+    usedefault=True,
+    ),
+    reg_file=dict(argstr='--reg %s',
+    mandatory=True,
+    name_source='fsl',
+    name_template='%s.dat',
+    ),
+    subject_id=dict(argstr='--s %s',
+    mandatory=True,
+    ),
+    subjects_dir=dict(),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    )
+    inputs = Tkregister2.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_Tkregister2_outputs():
+    output_map = dict(reg_file=dict(),
+    )
+    outputs = Tkregister2.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/freesurfer/utils.py

@@ -1188,3 +1188,42 @@ class ExtractMainComponent(CommandLine):
     _cmd='mris_extract_main_component'
     input_spec=ExtractMainComponentInputSpec
     output_spec=ExtractMainComponentOutputSpec
+
+
+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')
+    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')
+
+
+class Tkregister2(FSCommand):
+    """Use tkregister2 without the manual editing stage to convert 
+    FSL-style registration matrix (.mat) to FreeSurfer-style registration matrix (.dat)
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.freesurfer import Tkregister2
+    >>> tk2 = Tkregister2(reg_file='register.dat')
+    >>> tk2.inputs.moving_image = 'epi.nii'
+    >>> tk2.inputs.fsl_in_matrix = 'flirt.mat'
+    >>> tk2.inputs.subject_id = 'test_subject'
+    >>> tk2.run() # doctest: +SKIP
+    """
+    _cmd = "tkregister2"
+    input_spec = Tkregister2InputSpec
+    output_spec = Tkregister2OutputSpec
+    
+
+