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Hi Doug,
Thank you for your suggestions, I'll try them. Could you please let me know if my code is actually doing what I intend it to do? Specifically, the idea is to perform functional-to-structural registration.
so first I did $ bbregister --t2 --reg /data/bbregister/reg.dat --mov /data/mean_func.nii.gz --s 001
I'm not sure if the --mov image should be the motion-corrected mean functional image or the skull-stripped anatomical image. I think if I want to do functional-to-structural registration it should actually be the anatomical image as --mov right? Or it doesn't matter which one I choose?
I then did $ mri_vol2vol --mov /data/bet_structural.nii.gz --targ /data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg /data/bbregister/reg.dat --inv –-nearest which I thinks applies the transformation matrix to the structural image, am I correct? In this case it would be a structural-to-functional registration I think. So, if I intend to perform functional-to-structural registration I should actually rather do
$ bbregister --t2 --reg /data/bbregister/reg.dat --mov /data/bet_structural.nii.gz --s 001 $ mri_vol2vol --mov /data/mean_func.nii.gz --targ /data/brain.nii.gz --o /data/coregistered_functional.nii.gz --reg /data/bbregister/reg.dat --inv –-nearest
Could you please confirm if this is correct?
Thank you very much, Ben
Sometimes the FSL initialization will fail. If you are using FS version 6, then run it without specifying --init-fsl and it will use mri_coreg, which is more robust. If your anatomical and functional were acquired at the same time, you might be able to get away with --init-header instead.
On 8/9/18 2:12 PM, Ben M wrote:
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*>>* Hi, *>* I'm trying to coregister the strucural image to the mean functional *>* image using bbregister, so after reconall I did: *>>* bbregister --t2 --init-fsl --reg /data/bbregister/reg.dat --mov *>* /data/mean_func.nii.gz --s 001 *>>* bet /data/structural.nii.gz /data/bet_structural.nii.gz *>>* #brain.nii.gz is the brain.mgz from reconall output (in freesurfer space) *>* mri_vol2vol --mov /data/bet_structural.nii.gz --targ *>* /data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg *>* /data/bbregister/reg.dat --inv –-nearest *>>* But when I load the coregistered_structural.nii.gz and the *>* mean_func.nii.gz they are not aligned. I'm sure I'm doing something *>* wrong, could someone help me figure it out please? *>>* Thanks in advance, *>* Ben*