Dear FSL experts,
I want to co-register a T1 file to a 4D epi file. (The epi files are already co-registered). The problem is that the T1 should remain in its original spacing.
I tried the following:
1) create an empty file with a the following header that matches the header of the T1 image:
fslcreatehd 160 256 256 1 1 0.94 0.94 1 0 0 0 16 header.nii.gz
2) calculate the rigid transformation:
flirt -dof 6 -in T1.nii.gz -ref EPI.nii.gz -omat rigid_trans.mat -out
3) apply the transformation with the header file as reference:
flirt -in T1.nii.gz -ref header.nii.gz -applyxfm -init rigid_trans.mat -out flirt_T1.nii.gz
I tried 3) both with and without "-applyxfm". Both outcomes were not what I hoped for.
Could somebody please point me in the right direction?
Thanks, Vincent
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