Dear Freesurfer experts,
I am currently trying to segment a 7T image at 0.8 isotropic resolution. I have an MPRAGE scan and a Gradient echo, and want to coregister the data before processing to correct for inhomogenities, but unsure whether I can use FSL instead of SPM. I am following these instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
I am new to SP8 and not sure what I would have to do with this information specifically: (i1./i2 .* (i2>20)) .* 100.
Also, is it possible to just use the recon-all process or would you recommend going through each step individually outlined above? Is the second option the option for keeping the voxels at 0.8? Furthermore, I read somewhere that you have to use the -cm -aseg command to keep the voxels the same. is this true?
Best wishes and many thanks, Lucy