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

* upstream/master: (22 commits)
  Reformated inputs and added tests
  fix: fixed autotest for applytopup
  Fixed file extension
  Fixed test files import.
  FIX: topup out file and params
  fixed possible values for -datatype parameter of tracks2prob interface. Previous values were in error. correct values obtained from: http://www.brain.org.au/software/mrtrix/general/formats.html#datatypes
  fix: construct sparse matrix using topological sort order
  autogenerated tests
  added dummy files for testing new mrtrix interfaces
  updated CHANGES log
  Updated new mrtrix interfaces to new out_file format
  Added GenerateDirections, FindShPeaks, Directions2Amplitude interfaces wrapping gendir, find_SH_peaks and dir2amp mrtrix commands.
  Removed ipdb trace
  Fixing path issues for CMTK Parcellate dilated ROI files
  tst: auto test generation for FUGUE
  fix: warp/unwarp arg parsing for use w/o an in_file
  fix: typo in fugue parameter
  add: pycharm .idea/ directory to .gitignore
  fixed errors from DOCTEST, now OK.
  fixed pull request issues: wrapping Surface2VolTransform, -moved from preprocess.py to utils.py -improved input descriptions -renamed output suffix
  ...

Author: satra

.gitignore

@@ -12,3 +12,4 @@
 .project
 .settings
 .pydevproject
+.idea/

CHANGES

@@ -8,7 +8,6 @@ Next release
 * ENH: Added support for Simple Linux Utility Resource Management (SLURM)
 * ENH: AFNI interfaces refactor, prefix, suffix are replaced by "flexible_%s_templates"
 * ENH: DataGrabber and SelectFiles use human (or natural) sort now
-
 * ENH: Several new interfaces related to Camino were added:
         - camino.SFPICOCalibData
         - camino.Conmat
@@ -17,6 +16,10 @@ Next release
         - camino.SFPeaks
         One outdated interface no longer part of Camino was removed:
         - camino.Conmap
+* ENH: Three new mrtrix interfaces were added:
+        - mrtrix.GenerateDirections
+        - mrtrix.FindShPeaks
+        - mrtrix.Directions2Amplitude
 
 * FIX: Several fixes related to Camino interfaces:
         - ProcStreamlines would ignore many arguments silently (target, waypoint, exclusion ROIS, etc.)

nipype/interfaces/afni/preprocess.py

@@ -330,7 +330,6 @@ class AutoTcorrelateInputSpec(AFNICommandInputSpec):
     mask_only_targets = traits.Bool(desc="use mask only on targets voxels",
                                     argstr="-mask_only_targets",
                                     xor=['mask_source'])
-
     mask_source = File(exists=True,
                         desc="mask for source voxels",
                         argstr="-mask_source %s",

nipype/interfaces/cmtk/parcellation.py

@@ -258,7 +258,7 @@ def create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation):
             rois[idx] = int(brv['dn_correspondence_id'])
 
         # store volume eg in ROI_scale33.nii.gz
-        out_roi = op.join(output_dir, 'ROI_%s.nii.gz' % parcellation_name)
+        out_roi = op.abspath('ROI_%s.nii.gz' % parcellation_name)
 
         # update the header
         hdr = aseg.get_header()
@@ -290,7 +290,7 @@ def create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation):
                 rois[xx[j], yy[j], zz[j]] = value
 
         # store volume eg in ROIv_scale33.nii.gz
-        out_roi = op.join(output_dir, 'ROIv_%s.nii.gz' % parcellation_name)
+        out_roi = op.abspath('ROIv_%s.nii.gz' % parcellation_name)
         iflogger.info("Save output image to %s" % out_roi)
         img = nb.Nifti1Image(rois, aseg.get_affine(), hdr2)
         nb.save(img, out_roi)
@@ -303,7 +303,6 @@ def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
     fs_dir = op.join(subjects_dir, subject_id)
     cmp_config = cmp.configuration.PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
-    log = cmp_config.get_logger()
     pgpath = cmp_config._get_lausanne_parcellation(
         'Lausanne2008')[parcellation_name]['node_information_graphml']
     # load ribbon as basis for white matter mask
@@ -422,8 +421,6 @@ def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
     wmmask[idx] = 1
 
     # check if we should subtract the cortical rois from this parcellation
-    parval = cmp_config._get_lausanne_parcellation(
-        'Lausanne2008')[parcellation_name]
     iflogger.info("Loading %s to subtract cortical ROIs from white matter mask" % ('ROI_%s.nii.gz' % parcellation_name))
     roi = nb.load(op.join(op.curdir, 'ROI_%s.nii.gz' % parcellation_name))
     roid = roi.get_data()
@@ -448,28 +445,25 @@ def crop_and_move_datasets(subject_id, subjects_dir, fs_dir, parcellation_name,
     cmp_config = cmp.configuration.PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
     log = cmp_config.get_logger()
-    pgpath = cmp_config._get_lausanne_parcellation(
-        'Lausanne2008')[parcellation_name]['node_information_graphml']
-    reg_path = out_roi_file
     output_dir = op.abspath(op.curdir)
 
     iflogger.info("Cropping and moving datasets to %s" % output_dir)
     ds = [
-        (op.join(fs_dir, 'mri', 'aseg.nii.gz'), op.join(
-         output_dir, 'aseg.nii.gz')),
-        (op.join(fs_dir, 'mri', 'ribbon.nii.gz'), op.join(
-         output_dir, 'ribbon.nii.gz')),
-        (op.join(fs_dir, 'mri', 'fsmask_1mm.nii.gz'), op.join(
-         output_dir, 'fsmask_1mm.nii.gz')),
+        (op.join(fs_dir, 'mri', 'aseg.nii.gz'),
+         op.abspath('aseg.nii.gz')),
+        (op.join(fs_dir, 'mri', 'ribbon.nii.gz'),
+         op.abspath('ribbon.nii.gz')),
+        (op.join(fs_dir, 'mri', 'fsmask_1mm.nii.gz'),
+         op.abspath('fsmask_1mm.nii.gz')),
         (op.join(fs_dir, 'label', 'cc_unknown.nii.gz'),
-         op.join(output_dir, 'cc_unknown.nii.gz'))
+         op.abspath('cc_unknown.nii.gz'))
     ]
 
-    ds.append((op.join(op.curdir, 'ROI_%s.nii.gz' % parcellation_name),
-              op.join(op.curdir, 'ROI_HR_th.nii.gz')))
+    ds.append((op.abspath('ROI_%s.nii.gz' % parcellation_name),
+              op.abspath('ROI_HR_th.nii.gz')))
     if(dilation==True):
-    	ds.append((op.join(op.curdir, 'ROIv_%s.nii.gz' %
-              parcellation_name), op.join(op.curdir, 'ROIv_HR_th.nii.gz')))
+    	ds.append((op.abspath('ROIv_%s.nii.gz' % parcellation_name),
+            op.abspath('ROIv_HR_th.nii.gz')))
     orig = op.join(fs_dir, 'mri', 'orig', '001.mgz')
     for d in ds:
         iflogger.info("Processing %s:" % d[0])

nipype/interfaces/freesurfer/__init__.py

@@ -4,12 +4,12 @@
 
 from .base import Info, FSCommand
 from .preprocess import (ParseDICOMDir, UnpackSDICOMDir, MRIConvert, Resample,
-                         ReconAll, BBRegister, ApplyVolTransform, Smooth,
+                         ReconAll, BBRegister, ApplyVolTransform,Smooth,
                          DICOMConvert, RobustRegister, FitMSParams,
                          SynthesizeFLASH)
 from .model import (MRISPreproc, GLMFit, OneSampleTTest, Binarize, Concatenate,
                     SegStats, Label2Vol, MS_LDA)
-from .utils import (SampleToSurface, SurfaceSmooth, SurfaceTransform,
+from .utils import (SampleToSurface, SurfaceSmooth, SurfaceTransform, Surface2VolTransform, 
                     SurfaceSnapshots,ApplyMask, MRIsConvert, MRITessellate,
                     MRIMarchingCubes, SmoothTessellation, MakeAverageSubject,
                     ExtractMainComponent)

nipype/interfaces/freesurfer/preprocess.py

@@ -970,7 +970,6 @@ class ApplyVolTransformInputSpec(FSTraitedSpec):
                                      'non-linear morph to resample the input '
                                      'volume. To be used by --m3z.'))
 
-
 class ApplyVolTransformOutputSpec(TraitedSpec):
     transformed_file = File(exists=True, desc='Path to output file if used normally')
 
@@ -1021,7 +1020,6 @@ def _gen_filename(self, name):
             return self._get_outfile()
         return None
 
-
 class SmoothInputSpec(FSTraitedSpec):
     in_file = File(exists=True, desc='source volume',
                      argstr='--i %s', mandatory=True)

nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py

@@ -0,0 +1,66 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.freesurfer.utils import Surface2VolTransform
+def test_Surface2VolTransform_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    transformed_file=dict(name_source=['source_file'],
+    hash_files=False,
+    name_template='%s_asVol.nii',
+    argstr='--outvol %s',
+    ),
+    hemi=dict(mandatory=True,
+    argstr='--hemi %s',
+    ),
+    template_file=dict(argstr='--template %s',
+    ),
+    subject_id=dict(xor=['reg_file'],
+    argstr='--identity %s',
+    ),
+    args=dict(argstr='%s',
+    ),
+    surf_name=dict(argstr='--surf %s',
+    exists=True,
+    ),
+    vertexvol_file=dict(name_source=['source_file'],
+    hash_files=False,
+    name_template='%s_asVol_vertex.nii',
+    argstr='--vtxvol %s',
+    ),
+    reg_file=dict(mandatory=True,
+    argstr='--volreg %s',
+    xor=['subject_id'],
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    subjects_dir=dict(argstr='--sd %s',
+    ),
+    source_file=dict(copyfile=False,
+    mandatory=True,
+    argstr='--surfval %s',
+    ),
+    projfrac=dict(argstr='--projfrac %s',
+    exists=True,
+    ),
+    mkmask=dict(argstr='--mkmask',
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    )
+    inputs = Surface2VolTransform.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_Surface2VolTransform_outputs():
+    output_map = dict(transformed_file=dict(),
+    vertexvol_file=dict(),
+    )
+    outputs = Surface2VolTransform.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

@@ -382,6 +382,55 @@ def _gen_filename(self, name):
             return self._list_outputs()[name]
         return None
 
+class Surface2VolTransformInputSpec(FSTraitedSpec):
+    source_file = File(exists=True, argstr='--surfval %s',
+                      copyfile=False, mandatory=True,
+                      desc='This is the source of the surface values')
+    hemi = traits.Str(argstr='--hemi %s', mandatory=True, desc='hemisphere of data')
+    transformed_file = File(name_template="%s_asVol.nii", desc='Output volume', argstr='--outvol %s',
+                            name_source=['source_file'], hash_files=False)
+    reg_file = File(exists=True, argstr='--volreg %s',
+                    mandatory=True,
+                    desc='tkRAS-to-tkRAS matrix   (tkregister2 format)',
+                    xor=['subject_id'])
+    template_file = File(exists=True, argstr='--template %s',
+                      desc='Output template volume')
+    mkmask = traits.Bool(desc='make a mask instead of loading surface values', argstr='--mkmask')
+    vertexvol_file = File(name_template="%s_asVol_vertex.nii", desc='Path name of the vertex output '
+                          'volume, which is the same as output volume except that the value of each '
+                          'voxel is the vertex-id that is mapped to that voxel.',
+                          argstr='--vtxvol %s', name_source=['source_file'], hash_files=False)
+    surf_name = traits.Str(exists=True, argstr='--surf %s',desc='surfname (default is white)')
+    projfrac = traits.Float(exists=True, argstr='--projfrac %s',desc='thickness fraction')
+    subjects_dir = traits.Str(argstr='--sd %s',desc='freesurfer subjects directory defaults to $SUBJECTS_DIR')
+    subject_id = traits.Str(argstr='--identity %s',desc='subject id', xor=['reg_file'])
+
+class Surface2VolTransformOutputSpec(TraitedSpec):
+    transformed_file = File(exists=True, desc='Path to output file if used normally')
+    vertexvol_file = File(desc='vertex map volume path id. Optional')
+
+class Surface2VolTransform(FSCommand):
+    """Use FreeSurfer mri_surf2vol to apply a transform.
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.freesurfer import Surface2VolTransform
+    >>> xfm2vol = Surface2VolTransform()
+    >>> xfm2vol.inputs.source_file = 'lh.cope1.mgz'
+    >>> xfm2vol.inputs.reg_file = 'register.mat'
+    >>> xfm2vol.inputs.hemi = 'lh'
+    >>> xfm2vol.inputs.template_file = 'cope1.nii.gz'
+    >>> xfm2vol.inputs.subjects_dir = '.'
+    >>> xfm2vol.cmdline
+    'mri_surf2vol --hemi lh --volreg register.mat --surfval lh.cope1.mgz --sd . --template cope1.nii.gz --outvol lh.cope1_asVol.nii --vtxvol lh.cope1_asVol_vertex.nii'
+    >>> res = xfm2vol.run()# doctest: +SKIP
+
+    """
+
+    _cmd = 'mri_surf2vol'
+    input_spec = Surface2VolTransformInputSpec
+    output_spec = Surface2VolTransformOutputSpec
 
 class ApplyMaskInputSpec(FSTraitedSpec):
 

nipype/interfaces/fsl/epi.py

@@ -169,7 +169,9 @@ def _parse_inputs( self, skip=None ):
             skip = []
 
         if not isdefined(self.inputs.out_base ):
-            self.inputs.out_base = os.path.abspath( './nipypetu' )
+            self.inputs.out_base = './nipypetu'
+
+        self.inputs.out_base = os.path.abspath(self.inputs.out_base)
 
         if isdefined( self.inputs.encoding_file ):
             skip.append( 'encoding_direction' )
@@ -238,8 +240,8 @@ class ApplyTOPUPInputSpec( FSLCommandInputSpec ):
     in_topup = File( mandatory=True, desc='basename of field/movements (from topup)', argstr='--topup=%s' )
 
     out_base = File( desc='basename for output (warped) image', argstr='--out=%s' )
-    method = traits.Enum( ('jac','lsr'), argstr='-m=%s', desc='use jacobian modulation (jac) or least-squares resampling (lsr)' )
-    interp = traits.Enum( ('trilinear','spline'), argstr='-n=%s', desc='interpolation method' )
+    method = traits.Enum( ('jac','lsr'), argstr='--method=%s', desc='use jacobian modulation (jac) or least-squares resampling (lsr)' )
+    interp = traits.Enum( ('trilinear','spline'), argstr='--interp=%s', desc='interpolation method' )
     datatype = traits.Enum( ('char', 'short', 'int', 'float', 'double' ), argstr='-d=%s', desc='force output data type' )
 
 
@@ -289,7 +291,9 @@ def _parse_inputs( self, skip=None ):
             skip = []
 
         if not isdefined(self.inputs.out_base ):
-            self.inputs.out_base = os.path.abspath( './nipypeatu' )
+            self.inputs.out_base = './nipypeatu'
+
+        self.inputs.out_base = os.path.abspath(self.inputs.out_base)
         return super(ApplyTOPUP, self)._parse_inputs(skip=skip)
 
 

nipype/interfaces/fsl/preprocess.py

@@ -1197,7 +1197,7 @@ class FUGUEInputSpec(FSLCommandInputSpec):
                                desc='apply Fourier (sinusoidal) fitting of order N')
     pava = traits.Bool(argstr='--pava',
                        desc='apply monotonic enforcement via PAVA')
-    despike_theshold = traits.Float(argstr='--despikethreshold=%s',
+    despike_threshold = traits.Float(argstr='--despikethreshold=%s',
                                     desc='specify the threshold for de-spiking (default=3.0)')
     unwarp_direction = traits.Enum('x', 'y', 'z', 'x-', 'y-', 'z-',
                                    argstr='--unwarpdir=%s',
@@ -1287,13 +1287,13 @@ def _parse_inputs(self, skip=None):
                 self.inputs.shift_out_file = self._gen_fname(
                     self.inputs.in_file, suffix='_vsm')
 
-        if self.inputs.forward_warping or not isdefined(self.inputs.in_file):
-            skip += ['unwarped_file']
+        if not isdefined(self.inputs.in_file):
+            skip += ['unwarped_file', 'warped_file']
+        elif self.inputs.forward_warping:
             if not isdefined(self.inputs.warped_file):
                 self.inputs.warped_file = self._gen_fname(
                     self.inputs.in_file, suffix='_warped')
-        if not self.inputs.forward_warping or not isdefined(self.inputs.in_file):
-            skip += ['warped_file']
+        elif not self.inputs.forward_warping:
             if not isdefined(self.inputs.unwarped_file):
                 self.inputs.unwarped_file = self._gen_fname(
                     self.inputs.in_file, suffix='_unwarped')