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 Caution
>
> 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 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
> > <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>
> >
> > _______________________________________________
> > Freesurfer mailing list
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>
>
> _______________________________________________
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> 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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