I am new to fsl so am definitely not the best person to answer this, but I think
you would want to edit your _struc_brain.nii.gz.
I am in a somewhat similar situation ... BET gives good results for me but we have
an in house procedure optimized for our data that includes BET and some other
things.
My question is similar: How should I edit the sienax script if I am using my own
brain extractions ... i.e. so the sienex script starts right after the BET stage?
Any advice would be greatly appreciated.
Best wishes,
Omar
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Omar Ghaffar
PhD Candidate
Institute of Medical Science
University of Toronto
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