Hi Brian,
Thanks for your reply. Yes the all_fast_origsegs and all_fast_firstseg do
not overlay. I ran
run_first_all -b -i input.img -o output
I did edit the run_first_all script to use different nmodes parameters than
the defaults. I also edited the first_flirt to use normmi cost function
because the default was not giving good registrations. I also used skull
stripped brains for input because the non-skull stripped were not always
providing good segmentations. Other than that though, no edits.
Thanks for any advice,
Jason
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