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]<mailto:[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]<mailto:[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]<mailto:[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
