 |
 |
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 ___________________________ Omar Ghaffar PhD Candidate Institute of Medical Science University of Toronto