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Interesting...I had a similar issue, but in my case full search + 12 dof worked. Not sure why this is giving you trouble. Another thing you could try is fslreorient2std before doing FLIRT. m- On Thu, Jun 6, 2013 at 11:20 AM, Rajani Sebastian-Vayttaden < [log in to unmask]> wrote: > The screen shot that i attached is registration using "Full Search". > > Thanks! > > > On Thu, Jun 6, 2013 at 1:53 PM, Manish Saggar <[log in to unmask]>wrote: > >> Try again with "Full Search" instead of "normal search" under the >> registration tab. >> >> m- >> >> >> On Thu, Jun 6, 2013 at 10:47 AM, Rajani Sebastian-Vayttaden < >> [log in to unmask]> wrote: >> >>> Hello All, >>> >>> I have a question regarding registration of images obtained in two >>> different sessions on the same day. I am involved in a longitudinal fMRI >>> study on language recovery post stroke. We collect several different scans >>> and the total scan time is about 2 hours. Because of the long scan time we >>> divide it into 2 or 3 session. We try to collect MPRAGE in each session so >>> it will be easier for registering the functional image obtained in the same >>> session. However, at times due to patient compliance and/or lack of time we >>> are not able to obtain structural scans in each session. When i tried to >>> register functional scans obtained in one session to structural scans >>> obtained in another using FLIRT, the registration is completely messed up. >>> I am attaching a screen shot. >>> Is there any way i can improve the registration quality without having >>> to collect structural scans in each session. >>> >>> Thanks, >>> >>> Rajani >>> >> >> >