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if the same person, you should use rigid body (6-parameter) registration. ;-) On Mon, Nov 18, 2013 at 3:35 PM, Ran Xu <[log in to unmask]> wrote: > Dear Jesper, > > Thanks for your reply. I checked the registered image volume and used > betted brains. They looks fine. Do you think I should use others, like > affine transformation with 12 dof to register these two brains? or still > just using the fslroi to cut the some slices? > Thanks again, > > Ran > > > On Sun, Nov 17, 2013 at 2:33 PM, Jesper Andersson < > [log in to unmask]> wrote: > >> Dear Ran, >> >> the first thing you need to check is if your image volumes are in >> register after running flirt. >> >> If they are it probably means you are doing something wrong when you >> apply the transform to our ROI. >> >> If they are not you should make sure that you have betted the images >> prior to running flirt. If you have (betted them) you should try to cut the >> 256 slice volume down to a more similar size, and above all z-location, by >> removing slices at top and/or bottom. You can use fslroi for that. >> >> Jesper >> >> On 17 Nov 2013, at 18:26, Ran Xu <[log in to unmask]> >> wrote: >> >> Dear Mark, >> >> I used the FLIRT GUI, and chose the "Rigid Body (6 parameter model)", >> other options are the default. And then I still used "Rigid Body (6 >> parameter model)" and tried the cost function "Mutual Information", and >> the result seems not so good. The ROI is still in misplacement. >> Could you give me some advice? >> Thank you very much, >> >> Ran >> >> >> On Sat, Nov 16, 2013 at 9:24 AM, Mark Jenkinson < >> [log in to unmask]> wrote: >> >>> Dear Ran, >>> >>> What commands did you run? >>> I found the description here unclear. >>> >>> All the best, >>> Mark >>> >>> >>> On 15 Nov 2013, at 20:32, Ran Xu <[log in to unmask]> wrote: >>> >>> > Dear FSL experts, >>> > >>> > I used FLIRT to register the different images of one person, >>> T1-weighted image and another T1-weighted image. These two images have the >>> same resolution 1x1x1, and different the image size, one is 256x256x256 in >>> Freesurfer space and the other is 256x256x150. Also, I applied this >>> transformation to a ROI in Freesurfer space and I used the rigid with 6 dof >>> option, but the results are wrong. >>> > Could someone tell me why this happened? >>> > >>> > Thanks, >>> > Ran >>> >> >> >> >