Hello Freesurfer Experts,

   As a follow up question for bbregister, I used the --tmp and --epi-mask options, but I did not see a mask in the directory.  I wanted to  see if there is any way to output the B0/edge excluded epi-mask used in bbregister?

Thanks,

Ajay

On Tue, Apr 5, 2016 at 11:03 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote:

Hi Freesurfer Experts,

   I was running bbregister and came across an issue.  I have used previous versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at it worked perfectly for a specific subject. 

I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm option with the same resting state scan, and it did not move at all.  When looking at the terminal I saw that when matlab started up within bbregister, the command fs_spmreg was not found.  I also installed spm8 and reran the subject with the same issue.  When I changed the option to --init-fsl everything worked. I checked the matlab installation and everything looks fine, so I think the issue may be the fs_spmreg function not being found.  I am not sure if there is an easy fix for this, but any help would be appreciated.

Thanks,

Ajay