Thanks for the follow up about the new tool you developed! I look forward to using it and I will remove the --init-spm option.
Just as a follow up I did add the pathway for freesurfer/matlab and it ran properly for hippocampal subfields, so I do not think that is the issue.
Thanks, Ajay
On Wed, Apr 6, 2016 at 12:59 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
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