External Email - Use Caution Thank you! Unfortunately, I don't have any whole brain scan. I registered the template and all the runs with tkregisterfv and the I run bbregsiter. Now, should I just re-run selxavg3-sess?
Thanks Best Il giorno lun 26 nov 2018 alle ore 22:31 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > 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 -- 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
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