Merge remote-tracking branch 'upstream/master' into enh/restingconn

* upstream/master: (27 commits)
  add: prov:type for activity that includes nipype module
  fix: attribute names are lowercase camelcase
  fix: class names are capitalized camelcase
  add missing argument to FLIRT
  simplified code
  auto_tests
  DcmStack: add option for unsetting force reading of files without DICM marker, skip gif images in input
  add PrepareFieldmap test
  update make specs
  add to CHANGES
  Polish interface, add examples, add tests
  modify manual test to pass with new ordering
  update make specs
  run make specs
  remove subjects dir from example too
  remove redundant subjects directory input
  modify example to pass test
  run make specs
  Remove position from --warp argument, not necessary
  create automatic test
  ...

Author: satra

CHANGES

@@ -1,6 +1,8 @@
 Next Release
 ============
 
+* ENH: New FSL interface: EpiReg
+* 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/dcmstack.py

@@ -22,6 +22,7 @@
                                    )
 import nibabel as nb
 from nipype.interfaces.traits_extension import isdefined, Undefined
+import imghdr
 
 have_dcmstack = True
 try:
@@ -83,6 +84,9 @@ class DcmStackInputSpec(NiftiGeneratorBaseInputSpec):
                                   "any default exclude filters")
     include_regexes = traits.List(desc="Meta data to include, overriding any "
                                   "exclude filters")
+    force_read = traits.Bool(True, usedefault=True, 
+                             desc=('Force reading files without DICM marker'))
+
 
 class DcmStackOutputSpec(TraitedSpec):
     out_file = File(exists=True)
@@ -125,8 +129,9 @@ def _run_interface(self, runtime):
                                                      include_regexes)
         stack = dcmstack.DicomStack(meta_filter=meta_filter)
         for src_path in src_paths:
-            src_dcm = dicom.read_file(src_path, force=True)
-            stack.add_dcm(src_dcm)
+            if not imghdr.what(src_path)=="gif":
+                src_dcm = dicom.read_file(src_path, force=self.inputs.force_read)
+                stack.add_dcm(src_dcm)
         nii = stack.to_nifti(embed_meta=True)
         nw = NiftiWrapper(nii)
         self.out_path = \

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/__init__.py

@@ -19,7 +19,7 @@
                     Complex, InvWarp, WarpUtils, ConvertWarp, WarpPoints, WarpPointsToStd)
 
 from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp,
-                  SigLoss, EddyCorrect)
+                  SigLoss, EddyCorrect, EpiReg)
 
 from .dti import (BEDPOSTX, DTIFit, ProbTrackX, ProbTrackX2,
                   VecReg, ProjThresh, FindTheBiggest, DistanceMap,

nipype/interfaces/fsl/epi.py

@@ -46,7 +46,7 @@ class PrepareFieldmapInputSpec(FSLCommandInputSpec):
                           usedefault=True,
                           desc=('do not perform sanity checks for image '
                                 'size/range/dimensions'))
-    out_fieldmap = File(argstr='%s', position=5,
+    out_fieldmap = File(argstr='%s', position=4,
                         desc='output name for prepared fieldmap')
 
 
@@ -534,6 +534,129 @@ def _gen_filename(self, name):
             return self._list_outputs()['out_file']
         return None
 
+
+class EpiRegInputSpec(FSLCommandInputSpec):
+    epi = File(exists=True, argstr='--epi=%s', mandatory=True,
+               position=-4, desc='EPI image')
+    t1_head = File(exists=True, argstr='--t1=%s', mandatory=True,
+                   position=-3, desc='wholehead T1 image')
+    t1_brain = File(exists=True, argstr='--t1brain=%s', mandatory=True,
+                    position=-2, desc='brain extracted T1 image')
+    out_base = traits.String(desc='output base name', argstr='--out=%s',
+                             position=-1)
+    fmap = File(exists=True, argstr='--fmap=%s',
+                desc='fieldmap image (in rad/s)')
+    fmapmag = File(exists=True, argstr='--fmapmag=%s',
+                   desc='fieldmap magnitude image - wholehead')
+    fmapmagbrain = File(exists=True, argstr='--fmapmagbrain=%s',
+                        desc='fieldmap magnitude image - brain extracted')
+    wmseg = File(exists=True, argstr='--wmseg=%s',
+                 desc='white matter segmentation of T1 image, has to be named \
+                 like the t1brain and end on _wmseg')
+    echospacing = traits.Float(argstr='--echospacing=%f',
+                               desc='Effective EPI echo spacing  \
+                               (sometimes called dwell time) - in seconds')
+    pedir = traits.Enum('x', 'y', 'z', '-x', '-y', '-z', argstr='--pedir=%s',
+                        desc='phase encoding direction, dir = x/y/z/-x/-y/-z')
+
+    weight_image = File(exists=True, argstr='--weight=%s',
+                      desc='weighting image (in T1 space)')
+    no_fmapreg = traits.Bool(False, argstr='--nofmapreg',
+                        desc='do not perform registration of fmap to T1 \
+                        (use if fmap already registered)')
+    no_clean = traits.Bool(False, argstr='--noclean',
+                        desc='do not clean up intermediate files')
+    
+
+class EpiRegOutputSpec(TraitedSpec):
+    out_file = File(exists=True,
+                    desc='unwarped and coregistered epi input')     
+    out_1vol = File(exists=True,
+                          desc='unwarped and coregistered single volume')
+    fmap2str_mat = File(exists=True,
+                        desc='rigid fieldmap-to-structural transform')
+    fmap2epi_mat = File(exists=True,
+                        desc='rigid fieldmap-to-epi transform')
+    fmap_epi = File(exists=True, desc='fieldmap in epi space')
+    fmap_str = File(exists=True, desc='fieldmap in structural space')
+    fmapmag_str = File(exists=True,
+                       desc='fieldmap magnitude image in structural space')
+    epi2str_inv = File(exists=True,
+                       desc='rigid structural-to-epi transform')
+    epi2str_mat = File(exists=True,
+                       desc='rigid epi-to-structural transform')
+    shiftmap = File(exists=True, desc='shiftmap in epi space')
+    fullwarp = File(exists=True,
+                    desc='warpfield to unwarp epi and transform into \
+                    structural space')
+    wmseg = File(exists=True, desc='white matter segmentation used in flirt bbr')
+    wmedge = File(exists=True, desc='white matter edges for visualization')
+
+
+class EpiReg(FSLCommand):
+    """
+
+    Runs FSL epi_reg script for simultaneous coregistration and fieldmap 
+    unwarping.
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.fsl import EpiReg
+    >>> epireg = EpiReg()
+    >>> epireg.inputs.epi='epi.nii'
+    >>> epireg.inputs.t1_head='T1.nii'
+    >>> epireg.inputs.t1_brain='T1_brain.nii'
+    >>> epireg.inputs.out_base='epi2struct'
+    >>> epireg.inputs.fmap='fieldmap_phase_fslprepared.nii'
+    >>> epireg.inputs.fmapmag='fieldmap_mag.nii'
+    >>> epireg.inputs.fmapmagbrain='fieldmap_mag_brain.nii'
+    >>> epireg.inputs.echospacing=0.00067
+    >>> epireg.inputs.pedir='y'
+    >>> epireg.cmdline #doctest: +ELLIPSIS
+    'epi_reg --echospacing=0.000670 --fmap=fieldmap_phase_fslprepared.nii \
+--fmapmag=fieldmap_mag.nii --fmapmagbrain=fieldmap_mag_brain.nii --pedir=y \
+--epi=epi.nii --t1=T1.nii --t1brain=T1_brain.nii --out=epi2struct'
+    >>> epireg.run() # doctest: +SKIP
+    
+    """
+    _cmd = 'epi_reg'
+    input_spec = EpiRegInputSpec
+    output_spec = EpiRegOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '.nii.gz')
+        outputs['out_1vol'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_1vol.nii.gz')
+        outputs['fmap2str_mat'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_fieldmap2str.mat')
+        outputs['fmap2epi_mat'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_fieldmaprads2epi.mat')
+        outputs['fmap_epi'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_fieldmaprads2epi.nii.gz')
+        outputs['fmap_str'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_fieldmaprads2str.nii.gz')
+        outputs['fmapmag_str'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_fieldmap2str.nii.gz')
+        outputs['epi2str_inv'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_inv.mat')
+        outputs['epi2str_mat'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '.mat')
+        outputs['shiftmap'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_fieldmaprads2epi_shift.nii.gz')
+        outputs['fullwarp'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_warp.nii.gz')
+        outputs['wmedge'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_fast_wmedge.nii.gz')
+        outputs['wmseg'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_fast_wmseg.nii.gz')
+
+        return outputs
+
+
+
 #######################################
 # deprecated interfaces
 #######################################

nipype/interfaces/fsl/preprocess.py

@@ -471,10 +471,12 @@ class FLIRTInputSpec(FSLCommandInputSpec):
                                    desc='do not use blurring on downsampling')
     rigid2D = traits.Bool(argstr='-2D',
                           desc='use 2D rigid body mode - ignores dof')
-
     save_log = traits.Bool(desc='save to log file')
     verbose = traits.Int(argstr='-verbose %d',
                          desc='verbose mode, 0 is least')
+    bgvalue = traits.Float(0, argstr='-setbackground %f',
+                           desc=('use specified background value for points '
+                                 'outside FOV'))
 
     # BBR options
     wm_seg = File(
@@ -941,18 +943,18 @@ 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 +971,7 @@ 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')