nipype.interfaces.robex.preprocess module

RobexSegment

Link to code

Bases: CommandLine

Wrapped executable: runROBEX.sh.

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

>>> from nipype.interfaces.robex.preprocess import RobexSegment
>>> robex = RobexSegment()
>>> robex.inputs.in_file = 'structural.nii'
>>> robex.cmdline
'runROBEX.sh structural.nii structural_brain.nii structural_brainmask.nii'
>>> robex.run() 
Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Input volume. Maps to a command-line argument: %s (position: 0).

Optional Inputs:
  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • out_file (a pathlike object or string representing a file) – Output volume. Maps to a command-line argument: %s (position: 1).

  • out_mask (a pathlike object or string representing a file) – Output mask. Maps to a command-line argument: %s (position: 2).

  • seed (an integer) – Seed for random number generator. Maps to a command-line argument: %i (position: 3).

Outputs:
  • out_file (a pathlike object or string representing a file) – Output volume.

  • out_mask (a pathlike object or string representing a file) – Output mask.