using FSL bet

[khchuang]

I have fsl installed and followed the instructions on FSL website to setup environment variables and path in Matlab. However, sepia seems unable to find BET. There is also no path setting for BET in sepia. Please advise on how to set up FSL path to use BET in sepia.

[khchuang]

Found the solution in error message. Need to recompile the MEX of BET in the sepia.

[kschan0214]

Hi,

Are you able to resolve the issue?

SEPIA utilises the BET implementation on Matlab from the MEDI toolbox (https://pre.weill.cornell.edu/mri/pages/qsm.html) instead of the original implementation in FSL. Therefore, BET should work even without FSL installation as long as you have the MEDI toolbox available. (Of course if you have FSL installed then you can always use its unix command to derive the brain mask and provide this data as part of the SEPIA input.)

Kwok