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Thank you! Now the registration is better but still not perfect. Is there a way to improve it?
Best
Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2 weighted? If so, you should use --t2 instead of --t1 in bbregister
On 2/14/19 2:18 PM, Francesca Strappini wrote:
External Email - Use CautionHi Doug,
Could you advise me about how to correctly run mri_vol2vol? The functional data did not get perfectly registered to the anatomy so I'm afraid I'm not running it correctly.
Thanks!
Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> ha scritto:
Hi Francesca sorry, I defer to Doug on the details of mri_vol2vol. cheers Bruce On Tue, 12 Feb 2019, Francesca Strappini wrote: > > External Email - Use Caution > > Thank you for the reply! > I run: > mri_vol2vol --reg register.dat --mov func_data.nii.gz --targ > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o func_data_registered2T1.nii.gz --no-resample > > Then I checked the registration and it seems that the original run is better aligned to the T1 than > the registered one. Maybe am I not running mri_vol2vol correctly? > > Thanks! > Best > > > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> ha scritto: > Hi Francesca > > check out the --no-resample option in mri_vol2vol. It just changes the > header, so I think should do what you want. > > cheers > Bruce > > > On Tue, 12 Feb 2019, Francesca Strappini wrote: > > > > > External Email - Use Caution > > > > Dear Freesurfer's experts, > > > > I would like to register some functional data to the T1, that were collected in > separate days. > > I used bbregister: > > > > bbregister --s sub3 --mov func_data.nii.gz - --reg register.dat --init-coreg --t1 > > > > Now, I would like to resample the data based on the register.dat without upsampling > and keeping the > > same FoV (3x3x3 mm; 64 64 50). Is it doable? > > > > Thanks! > > Best > > > > > > -- > > 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> > > > >_______________________________________________ > 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.strappini@weizmann.ac.il <mailto:francesca.strappini@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-- 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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