Added robex segment interface

Author: mfmachado

nipype/interfaces/robex/__init__.py

@@ -0,0 +1,70 @@
+import os
+from pathlib import Path
+
+from nipype.interfaces.base import (
+    TraitedSpec,
+    CommandLineInputSpec,
+    CommandLine,
+    File,
+    traits, isdefined
+)
+from nipype.utils.filemanip import split_filename
+
+
+class RobexInputSpec(CommandLineInputSpec):
+    in_file = File(desc="Input volume", exists=True,
+                   mandatory=True, position=0, argstr="%s")
+    out_file = File(desc="Output volume", position=1, argstr="%s",
+                    hash_files=False, name_template='%s_brain', keep_extension=True)
+    out_mask = File(desc="Output mask", position=2, argstr="%s",
+                    hash_files=False, name_template='%s_brainmask', keep_extension=True)
+    seed = traits.Int(desc="Seed for random number generator", position=3, argstr="%i")
+
+
+class RobexOutputSpec(TraitedSpec):
+    out_file = File(desc="Output volume", exists=True)
+    out_mask = File(desc="Output mask", exists=True)
+
+
+class RobexSegment(CommandLine):
+    """
+
+    ROBEX is an automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping).
+    ROBEX aims for robust skull-stripping across datasets with no parameter settings. It fits a triangular mesh,
+    constrained by a shape model, to the probabilistic output of a supervised brain boundary classifier.
+    Because the shape model cannot perfectly accommodate unseen cases, a small free deformation is subsequently allowed.
+    The deformation is optimized using graph cuts.
+    The method ROBEX is based on was published in IEEE Transactions on Medical Imaging;
+    please visit the website http://www.jeiglesias.com to download the paper.
+
+        Examples
+    --------
+    >>> path_mr = 'structural.nii'
+    >>> robex = RobexSegment(in_file=path_mr)
+    >>> robex.run() # doctest: +SKIP
+
+    """
+
+    input_spec = RobexInputSpec
+    output_spec = RobexOutputSpec
+    _cmd = 'runROBEX.sh'
+
+    def _format_arg(self, name, trait_spec, value):
+        if name == "out_file" or name == "out_mask":
+            if Path(value).name == value:
+                value = os.path.join(os.getcwd(), Path(value).name)
+                setattr(self.inputs, name, value)
+        return super(RobexSegment, self)._format_arg(name, trait_spec, value)
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs["out_file"] = self.inputs.out_file
+        if isdefined(self.inputs.out_mask):
+            outputs["out_mask"] = self.inputs.out_mask
+        return outputs
+
+    def run(self, cwd=None, ignore_exception=None, **inputs):
+        if not isdefined(self.inputs.out_file):
+            _, base, extension = split_filename(self.inputs.in_file)
+            self.inputs.out_file = base + "_brain_robex_" + extension
+        return super(RobexSegment, self).run(cwd, ignore_exception, **inputs)