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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer