Merge branch 'master' into enh/NewEPIArtifactCorrections

Conflicts:
	CHANGES

Author: oesteban

CHANGES

@@ -3,6 +3,7 @@ Next Release
 
 * ENH: Deep revision of workflows for correction of dMRI artifacts. New dmri_preprocessing
        example.
+* 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/preprocess.py

@@ -807,7 +807,7 @@ class BBRegisterInputSpec(FSTraitedSpec):
     init = traits.Enum('spm', 'fsl', 'header', argstr='--init-%s',
                        mandatory=True, xor=['init_reg_file'],
                        desc='initialize registration spm, fsl, header')
-    init_reg_file = File(exists=True,
+    init_reg_file = File(exists=True, argstr='--init-reg %s',
                          desc='existing registration file',
                          xor=['init'], mandatory=True)
     contrast_type = traits.Enum('t1', 't2', argstr='--%s',

nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py

@@ -20,7 +20,8 @@ def test_BBRegister_inputs():
     mandatory=True,
     xor=['init_reg_file'],
     ),
-    init_reg_file=dict(mandatory=True,
+    init_reg_file=dict(argstr='--init-reg %s',
+    mandatory=True,
     xor=['init'],
     ),
     intermediate_file=dict(argstr='--int %s',

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
+    
+
+    

nipype/interfaces/fsl/preprocess.py

@@ -941,18 +941,18 @@ def write_config(self, configfile):
 
 class ApplyWarpInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, argstr='--in=%s',
-                   mandatory=True,
+                   mandatory=True, position=0,
                    desc='image to be warped')
-    out_file = File(argstr='--out=%s', genfile=True,
+    out_file = File(argstr='--out=%s', genfile=True, position=2,
                     desc='output filename', hash_files=False)
     ref_file = File(exists=True, argstr='--ref=%s',
-                    mandatory=True,
+                    mandatory=True, position=1,
                     desc='reference image')
     field_file = File(exists=True, argstr='--warp=%s',
                       desc='file containing warp field')
     abswarp = traits.Bool(argstr='--abs', xor=['relwarp'],
                           desc="treat warp field as absolute: x' = w(x)")
-    relwarp = traits.Bool(argstr='--rel', xor=['abswarp'],
+    relwarp = traits.Bool(argstr='--rel', xor=['abswarp'], position=-1,
                           desc="treat warp field as relative: x' = x + w(x)")
     datatype = traits.Enum('char', 'short', 'int', 'float', 'double',
                            argstr='--datatype=%s',
@@ -969,7 +969,7 @@ class ApplyWarpInputSpec(FSLCommandInputSpec):
     mask_file = File(exists=True, argstr='--mask=%s',
                      desc='filename for mask image (in reference space)')
     interp = traits.Enum(
-        'nn', 'trilinear', 'sinc', 'spline', argstr='--interp=%s',
+        'nn', 'trilinear', 'sinc', 'spline', argstr='--interp=%s', position=-2,
         desc='interpolation method')
 
 

nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py

@@ -20,14 +20,17 @@ def test_ApplyWarp_inputs():
     ),
     in_file=dict(argstr='--in=%s',
     mandatory=True,
+    position=0,
     ),
     interp=dict(argstr='--interp=%s',
+    position=-2,
     ),
     mask_file=dict(argstr='--mask=%s',
     ),
     out_file=dict(argstr='--out=%s',
     genfile=True,
     hash_files=False,
+    position=2,
     ),
     output_type=dict(),
     postmat=dict(argstr='--postmat=%s',
@@ -36,8 +39,10 @@ def test_ApplyWarp_inputs():
     ),
     ref_file=dict(argstr='--ref=%s',
     mandatory=True,
+    position=1,
     ),
     relwarp=dict(argstr='--rel',
+    position=-1,
     xor=['abswarp'],
     ),
     superlevel=dict(argstr='--superlevel=%s',

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -455,17 +455,17 @@ def test_applywarp():
                               field_file = reffile,
                               **{name : settings[1]})
         if name == 'out_file':
-            realcmd = 'applywarp --warp=%s '\
-                      '--in=%s --out=%s '\
-                      '--ref=%s'%(reffile, infile,
+            realcmd = 'applywarp --in=%s '\
+                      '--ref=%s --out=%s '\
+                      '--warp=%s'%(infile, reffile,
                                   settings[1],reffile)
         else:
             outfile = awarp._gen_fname(infile, suffix='_warp')
-            realcmd = 'applywarp --warp=%s '\
-                      '--in=%s --out=%s '\
-                      '%s --ref=%s'%(reffile, infile,
-                                     outfile, settings[0],
-                                     reffile)
+            realcmd = 'applywarp --in=%s '\
+                      '--ref=%s --out=%s '\
+                      '--warp=%s %s'%(infile, reffile,
+                                     outfile, reffile,
+                                     settings[0])
         yield assert_equal, awarp.cmdline, realcmd
 
     awarp = fsl.ApplyWarp(in_file = infile,