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()
- 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.