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 Caution > > Hi 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 > <fis...@nmr.mgh.harvard.edu <mailto:fis...@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 > <fis...@nmr.mgh.harvard.edu <mailto:fis...@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.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 > > > > > > > > -- > > 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 <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
