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. > <dgr...@mgh.harvard.edu <mailto:dgr...@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.strapp...@weizmann.ac.il > <mailto:francesca.strapp...@weizmann.ac.il> > > <mailto:francesca.strapp...@weizmann.ac.il > <mailto:francesca.strapp...@weizmann.ac.il>> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 > E-mail: francesca.strapp...@weizmann.ac.il > <mailto:francesca.strapp...@weizmann.ac.il> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
