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:
External Email - Use Caution
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
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