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# 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()

> 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.