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>
>     >       >
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>     >
>     >
>     >
>     > --
>     > 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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>
>
>
> --
> 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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