21 Feb
2019
21 Feb
'19
12:39 p.m.
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>> > > > > > > > >_______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <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>> > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <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>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > 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
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