External Email - Use Caution
I'll try to find some visual way to show what I mean, but it's really something mild and probably negligible. Do you know if is it possible with mri_vol2vol to give to all the runs that belong to the same subject the same system coordinates? So that each voxel across runs will have the same coordinates. I noticed that the transformation matrix is written in the header but it's not really applied to the data. Thank you!
Best Francesca
On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Francesca
can you send us an image that shows why you think it can be improved?
cheers Bruce On Mon, 18 Feb 2019, Francesca Strappini wrote:
External Email - Use CautionThank 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 Caution > > Hi Doug, > > Could you advise me about how to correctly run mri_vol2vol? > The functional data did not get perfectly registered to theanatomy 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 theoriginal
> run is better aligned to the T1 than > > the registered one. Maybe am I not running mri_vol2volcorrectly?
> > > > 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 tothe 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> > > _______________________________________________ > 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.strappini@weizmann.ac.il
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