--epi-mask is a simple flag without any options. It tells bbregsiter to exclude certain regions from the surface-based parcellation (?h.aparc.annot). The regions can be gleened from the code below

B0Annots[0] = CTABentryNameToAnnotation("middletemporal",lhwm->ct); B0Annots[1] = CTABentryNameToAnnotation("inferiortemporal",lhwm->ct); B0Annots[2] = CTABentryNameToAnnotation("temporalpole",lhwm->ct); B0Annots[3] = CTABentryNameToAnnotation("fusiform",lhwm->ct); B0Annots[4] = CTABentryNameToAnnotation("entorhinal",lhwm->ct); B0Annots[5] = CTABentryNameToAnnotation("medialorbitofrontal",lhwm->ct); B0Annots[6] = CTABentryNameToAnnotation("caudalanteriorcingulate",lhwm->ct); B0Annots[7] = CTABentryNameToAnnotation("rostralanteriorcingulate",lhwm->ct); B0Annots[8] = CTABentryNameToAnnotation("unknown",lhwm->ct); B0Annots[9] = CTABentryNameToAnnotation("corpuscallosum",lhwm->ct);

On 4/6/16 1:59 PM, Ajay Kurani 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 mailto: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

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