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Thanks so much! On Sat, Aug 1, 2009 at 5:33 AM, Mark Jenkinson <[log in to unmask]> wrote: > Hi Nicole, > > This looks fine to me. > Sometimes I would say that we get better results for step 1 > by using the skull-stripped image for T1High, but normally > it doesn't matter much as long as you stick to 6 DOF. > > Everything else looks great, so should work fine. > > All the best, > Mark > > > > On 1 Aug 2009, at 02:16, Nicole Strang wrote: > > Hi, >> I've primarily used afni in the past, but want to take advantage of the >> great non-linear registration in fsl. Because I've already run the >> first-level stats is afni, I'd like to use fsl for registration alone, if >> possible. I couldn't find an answer to my the question online, so I would >> really appreciate it if someone could let me know if there are any >> problems >> with my approach. If there is a problem, alternative would be very much >> appreciated. >> Convert all relevant files to NIFTI >> 1) Register run1 epi time series (there are 4 runs but all frames are >> aligned to first frame of run1) to skull on T1High (with flirt) >> 2) Register skull stripped T1High brain to MNI (with flirt) >> 3) Register skull on T1High to MNI (with fnirt) >> 4) Register output of glm which has been converted to percent signal >> change >> with output of (3) as warp and output of (1) as premat. >> >> Thanks! >> Nicole >> >> -- Nicole Strang Child Emotion Research Lab University of Wisconsin-Madison 1500 Highland Ave, Rm. 394 Madison, WI 53705 (608) 890-2525