And you only have partial field of view fmri data on that day? No whole
brain localizer? Really, any whole-brain volume will do. If you do not,
then you'll have to initialize the bbr registration by hand, which is a
bit of a pain. You'd run something like
tkregisterfv --mov template.nii.gz --init-header --reg manual.reg.lta
--surfs
Then adjust the registration to be within 5mm of being right. Then run
bbregister using that registration as the --init-reg
If you have other scans where you have both the partial FoV and a whole
brain, you might be able to get an init reg by registering the partial
FoVs from different days.
good luck



On 11/26/2018 03:19 PM, Francesca Strappini wrote:
>
>         External Email - Use Caution
>
> Thanks for the fast reply!
>
> Unfortunately, I have only 3 mprage scans that were collected in
> another day but no whole-head functional data.
>
> Il giorno lun 26 nov 2018 alle ore 22:07 Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> ha scritto:
>
>     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>
>     > <mailto:francesca.strappini@weizmann.ac.il
>     <mailto:francesca.strappini@weizmann.ac.il>>
>     >
>     >
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>
>
> --
> 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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