nipype.interfaces.robex.preprocess module¶
RobexSegment¶
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()
- in_filea pathlike object or string representing an existing file
Input volume. Maps to a command-line argument:
%s
(position: 0).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa 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_filea pathlike object or string representing a file
Output volume. Maps to a command-line argument:
%s
(position: 1).- out_maska pathlike object or string representing a file
Output mask. Maps to a command-line argument:
%s
(position: 2).- seedan integer
Seed for random number generator. Maps to a command-line argument:
%i
(position: 3).
- out_filea pathlike object or string representing a file
Output volume.
- out_maska pathlike object or string representing a file
Output mask.