Add 5ttgen interface

Author: oesteban

nipype/interfaces/mrtrix3/__init__.py

@@ -2,6 +2,6 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 # -*- coding: utf-8 -*-
 
-from utils import Mesh2PVE
+from utils import Mesh2PVE, Generate5tt
 from preprocess import ResponseSD, ACTPrepareFSL
 from tracking import Tractography

nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py

@@ -0,0 +1,43 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.mrtrix3.utils import Generate5tt
+
+def test_Generate5tt_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_fast=dict(argstr='%s',
+    mandatory=True,
+    position=-3,
+    ),
+    in_first=dict(argstr='%s',
+    position=-2,
+    ),
+    out_file=dict(argstr='%s',
+    mandatory=True,
+    position=-1,
+    usedefault=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = Generate5tt.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_Generate5tt_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = Generate5tt.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/mrtrix3/tracking.py

@@ -95,7 +95,7 @@ class TractographyInputSpec(CommandLineInputSpec):
         desc=('track from the seed point in one direction only '
               '(default is to track in both directions)'))
     init_dir = traits.Tuple(
-        traits.Float, traits.Float, traits.Float, 
+        traits.Float, traits.Float, traits.Float,
         argstr='-initdirection %f,%f,%f',
         desc=('specify an initial direction for the tracking (this '
               'should be supplied as a vector of 3 comma-separated values'))

nipype/interfaces/mrtrix3/utils.py

@@ -15,7 +15,8 @@
 import os.path as op
 
 from nipype.interfaces.base import (
-    CommandLineInputSpec, CommandLine, traits, TraitedSpec, File)
+    CommandLineInputSpec, CommandLine, traits, TraitedSpec, File,
+    InputMultiPath)
 
 from nipype.utils.filemanip import split_filename
 from nipype.interfaces.traits_extension import isdefined
@@ -55,7 +56,7 @@ class Mesh2PVE(CommandLine):
     >>> m2p.inputs.in_first = 'T1.nii.gz'
     >>> m2p.cmdline                               # doctest: +ELLIPSIS
     'mesh2pve -first T1.nii.gz surf1.vtk dwi.mif mesh2volume.nii.gz'
-    >>> resp.run()                                 # doctest: +SKIP
+    >>> m2p.run()                                 # doctest: +SKIP
     """
 
     _cmd = 'mesh2pve'
@@ -66,3 +67,50 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['out_file'] = op.abspath(self.inputs.out_file)
         return outputs
+
+
+class Generate5ttInputSpec(CommandLineInputSpec):
+    in_fast = InputMultiPath(
+        File(exists=True), argstr='%s', mandatory=True, position=-3,
+        desc='list of PVE images from FAST')
+    in_first = File(
+        exists=True, argstr='%s', position=-2,
+        desc='combined segmentation file from FIRST')
+    out_file = File(
+        'act-5tt.mif', argstr='%s', mandatory=True, position=-1,
+        usedefault=True, desc='name of output file')
+
+
+class Generate5ttOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='segmentation for ACT in 5tt format')
+
+
+class Generate5tt(CommandLine):
+
+    """
+    Concatenate segmentation results from FSL FAST and FIRST into the 5TT
+    format required for ACT
+
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.mrtrix3 as mrt
+    >>> seg = mrt.Generate5tt()
+    >>> seg.inputs.in_fast = ['tpm_00.nii.gz',
+    ...                       'tpm_01.nii.gz', 'tpm_02.nii.gz']
+    >>> seg.inputs.in_first = 'first_merged.nii.gz'
+    >>> seg.cmdline                               # doctest: +ELLIPSIS
+    '5ttgen tpm_00.nii.gz tpm_01.nii.gz tpm_02.nii.gz first_merged.nii.gz\
+ act-5tt.mif'
+    >>> seg.run()                                 # doctest: +SKIP
+    """
+
+    _cmd = '5ttgen'
+    input_spec = Generate5ttInputSpec
+    output_spec = Generate5ttOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = op.abspath(self.inputs.out_file)
+        return outputs