I reposted this message from a few days ago. Does anyone have some ideas? I attached the final image with this message.
Dear All,
I have registered a AAL template to FA image with the help from an expert, Emmanuel Vallee, in the List. And here is the commands:
fsl_reg <your_FA_image> ${FSLDIR}/data/standard/FMRIB58_FA_1mm.nii.gz FA_2_MNI -fnirt "--refmask=/usr/local/fsl/data/standard/MNI152_T1_1mm_brain_mask" -FA
invwarp -w FA_2_MNI_warp.nii.gz -r ${FSLDIR}/data/standard/FMRIB58_FA_1mm -o MNI_2_FA_warp
applywarp -i <atlas_in_MNI_space> -w MNI_2_FA_warp -r <your_FA_image> -o MNI_atlas_to_FA --interp=nn
The final image was relatively good, but the template exceeded the boundary along with the Z axis (superior-inferior) so that part of the top and bottom of the brain was missing. The FA dimensions was 128*128*70. FMRIB and MNI152 were 181*217*181. As the size of the output is based on the reference image, I tried to reigister the FA to T1 which was 255*255*255, generating a T1-weighted image, and use this instead of original FA and the final image was registered properly. But the same thing happened when I used ApplyXFM GUI to move it in a given space just like the FA.
How could I move the template back to the FA without any regions missing? Wish you could help me with it.
Best wishes,
Charlie
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