which betin the terminal that you are running the code in.
A) FSL installation is must even if we use nipype.interface for brain extration. FSL Installation link -> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation.
B) Add the following to ~/.bashrc file
export FSLDIR PATH
C) After complete installation restart the system.
Step 2: Check the installation :
A) Type FSL and press enter (BET tool (GUI)pops out).
B) In command prompt , type bet inputfilename.nii.gz outfilename
If it work well, then we can use nipype.interface program for multiple slice brain extraction .
Chris MarkiewiczNipype gives you the ability to easily switch from one tool to the other, if you decide one is better, but nipype has no way to determine "best" or automatically switch. You could create a workflow that performs several steps, and then selects one result using some objective function...