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.kur...@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.kur...@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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