External Email - Use Caution
Yes, if you run it with the --targ as orig.mgz for the given subject,
then it will sample each run into the anatomical space (this can create
enourmous data data files!). Alternatively, you can run preproc-sess
with the --per-session flag and it will align all the runs to a single
template but otherwise keep everything in the functional space
On 2/20/19 11:53 AM, Francesca Strappini wrote:
>
> 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 <mailto: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 <mailto: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>
> <mailto: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>
> <mailto: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>
> > > <mailto:francesca.strappini@weizmann.ac.il
> <mailto:francesca.strappini@weizmann.ac.il>>
> > > > >
> > > > >_______________________________________________
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> > > >
> 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>
> > > <mailto:francesca.strappini@weizmann.ac.il
> <mailto:francesca.strappini@weizmann.ac.il>>
> > > >
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> <mailto: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>
> > > <mailto: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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