Do you have any scan that was acquired at the same time that is whole
head? Any scan will do. If so, you can run register-sess using the
-bbr-int option (or bbregister directly). Eg, if the anatomical was
acquired at the same time, then, to use register-sess, create a folder
in the session folder called anatomical/001 and put the anatomical in
there (eg, anat.nii.gz), then use -bbr-int anatomical anat


On 11/26/2018 02:58 PM, Francesca Strappini wrote:
>
>         External Email - Use Caution
>
> Dear freesurfer experts,
>
> I am using freesurfer to analyze some fMRI data collected on two
> monkeys. My runs have a partial field of view, since just the
> posterior part of the brain was scanned. Unfortunately, no full-head
> EPI was collected. The registration between the processed functional
> data and the T1 is bad. All the values in the register.dof6.mincost
> file are above 0.8 and also visually I can see some mismatch. I though
> to run bbregister, could you suggest me which is the best procedure
> and which steps of the preprocessing I should re-run after?
>
> Thanks
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strappini@weizmann.ac.il
> <mailto:francesca.strappini@weizmann.ac.il>
>
>
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