Hello everybody,
I am sure, this question have been answered somewhere, but for some
reason I cannot find a similar topic in the forum archive.
Basically, I have a high resolution T1-weighted image (MPRAGE) and
would like to coregister a low resolution T2-weighted image to T1.
This is a standard problem.
I use flirt to do it and the result I get is T2 image rotated by 90
degrees around LR axis.
(see the attached image) Grayscale is T1 and color is T2.
The command which was used to attempt the coregistration is this
flirt -in t2image.nii.gz -ref t1image.nii.gz -out coregimg2 -omat
transformation2.mat -bins 256 -cost mutualinfo -searchrx -18 18
-searchry -18 18 -searchrz -18 18 -dof 12 -interp trilinear
-searchcost mutualinfo
Because the images intially a almost "coregistered" I have restricted
the angular search to speed up the calculation.
Could some one suggest what I did wrong or maybe some options which I
should use to attempt to resolve
the problem?
Thank you very much for your help
Lazar
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