[Freesurfer] Flags to align per-run motion-corrected functional volumes?

2012-03-06 Thread Alex Kell
Hi Freesurfers, I am using preproc-sess in Freesurfer/Fsfast 5 with per-run motion correction (these subjects have a lot of between-run motion), and I want to analyze the volumes in each subject's individual space (I'd prefer native functional space, but I am happy to do it in each subject's

Re: [Freesurfer] Flags to align per-run motion-corrected functional volumes?

2012-03-06 Thread Douglas N Greve
Hi Alex, analyzing in the anatomical space is going to be very, very costly in terms of space and memory (and I don't really have a way to do it). It is probably better to do it in mni305 space and turn off the masking out of cortex (-no-subcort-mask). You can then run reg-mni305.2mm to create