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
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
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> 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 CautionDear 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 > >_______________________________________________ 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
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> 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 CautionThank 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> ha scritto:
Hi Francesca check out the --no-resample option in mri_vol2vol. It just changesthe
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, thatwere 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.datwithout 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 > >_______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 CautionHi 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 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
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 > 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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External Email - Use Caution
Thanks a lot! Running preproc-sess with the --per-session flag is exactly was I was looking for! Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were created outside freesurfer. These regions are in volume space and have the same resolution and box size of the functional runs. They are registered to the T1 that was used for the reconstruction of the surface. I've tried different functions for the registration but nothing really worked. I suppose I need a registration matrix that relates these regions to the reference image I used during the preprocessing and to apply this to each region. What's the best procedure?
Best Francesca
Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
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 CautionI'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>
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There should be a registration file called register.dof6.lta. Use that with mri_label2vol passing your segmentation in with --seg. Run with --help to get more info
On 2/21/19 11:54 AM, Francesca Strappini wrote:
External Email - Use Caution
Thanks a lot! Running preproc-sess with the --per-session flag is exactly was I was looking for! Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were created outside freesurfer. These regions are in volume space and have the same resolution and box size of the functional runs. They are registered to the T1 that was used for the reconstruction of the surface. I've tried different functions for the registration but nothing really worked. I suppose I need a registration matrix that relates these regions to the reference image I used during the preprocessing and to apply this to each region. What's the best procedure?
Best Francesca
Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> ha scritto: 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 CautionI'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.edumailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edumailto: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> <mailto: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>> <mailto: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>> <mailto: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>> > > <mailto: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>> > > <mailto: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>> > > <mailto: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>> <mailto: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>> > > <mailto: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 > > > _______________________________________________ > 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
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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.ilmailto:francesca.strappini@weizmann.ac.il
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Thanks a lot, Doug! I run the preprocessing: preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session And the runs look well registered.
Then I run mri_label2vol: mri_label2vol --seg /home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz --reg register.dof6.lta --temp template.nii.gz --o sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz
The region is in the correct space but completely misaligned. The misalignment is even bigger than the unregistered region. Maybe I'm not running the function correctly. This set of regions are in the same space of the functional data but registered to the raw T1.
Best Francesca
Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
There should be a registration file called register.dof6.lta. Use that with mri_label2vol passing your segmentation in with --seg. Run with --help to get more info
On 2/21/19 11:54 AM, Francesca Strappini wrote:
External Email - Use CautionThanks a lot! Running preproc-sess with the --per-session flag is exactly was I was looking for! Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were created outside freesurfer. These regions are in volume space and have the same resolution and box size of the functional runs. They are registered to the T1 that was used for the reconstruction of the surface. I've tried different functions for the registration but nothing really worked. I suppose I need a registration matrix that relates these regions to the reference image I used during the preprocessing and to apply this to each region. What's the best procedure?
Best Francesca
Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
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 CautionI'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 beimproved?
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 runmri_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 BruceFischl
> > <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 Strappiniwrote:
> > > > > > > > > > > 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>
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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
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That looks right. Can you verify that the seg (sourcedata...) is in the conformed anatomical space? Use mri_info can compare the output (particularly the vox2ras matrix) against orig.mgz. If they are the same, you can try adding --invertmtx to the mri_label2vol command line.
On 2/22/19 2:24 PM, Francesca Strappini wrote:
External Email - Use Caution
Thanks a lot, Doug! I run the preprocessing: preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session And the runs look well registered.
Then I run mri_label2vol: mri_label2vol --seg /home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz --reg register.dof6.lta --temp template.nii.gz --o sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz
The region is in the correct space but completely misaligned. The misalignment is even bigger than the unregistered region. Maybe I'm not running the function correctly. This set of regions are in the same space of the functional data but registered to the raw T1.
Best Francesca
Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> ha scritto: There should be a registration file called register.dof6.lta. Use that with mri_label2vol passing your segmentation in with --seg. Run with --help to get more info
On 2/21/19 11:54 AM, Francesca Strappini wrote:
External Email - Use Caution
Thanks a lot! Running preproc-sess with the --per-session flag is exactly was I was looking for! Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were created outside freesurfer. These regions are in volume space and have the same resolution and box size of the functional runs. They are registered to the T1 that was used for the reconstruction of the surface. I've tried different functions for the registration but nothing really worked. I suppose I need a registration matrix that relates these regions to the reference image I used during the preprocessing and to apply this to each region. What's the best procedure?
Best Francesca
Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> ha scritto: 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 CautionI'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.edumailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edumailto: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> <mailto: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>> <mailto: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>> <mailto: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>> > > <mailto: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>> > > <mailto: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>> > > <mailto: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>> <mailto: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>> > > <mailto: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 > > > _______________________________________________ > 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
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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.ilmailto: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.ilmailto:francesca.strappini@weizmann.ac.il
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Thanks! The vox2ras matrices are not same.
This is one region:
francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz type: nii dimensions: 64 x 64 x 50 voxel sizes: 3.000000, 3.000000, 3.000000 type: FLOAT (3) fov: 192.000 dof: 0 xstart: -96.0, xend: 96.0 ystart: -96.0, yend: 96.0 zstart: -75.0, zend: 75.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9988, y_r = 0.0235, z_r = 0.0427, c_r = -2.2923 : x_a = 0.0124, y_a = 0.9702, z_a = -0.2420, c_a = 19.4768 : x_s = 0.0471, y_s = 0.2412, z_s = 0.9693, c_s = 25.1269 Orientation : LAS Primary Slice Direction: axial
voxel to ras transform: -2.9964 0.0704 0.1281 88.1380 0.0373 2.9106 -0.7261 -56.7017 0.1414 0.7237 2.9080 -75.2534 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -27
ras to voxel transform: -0.3329 0.0041 0.0157 30.7614 0.0078 0.3234 0.0804 23.6988 0.0142 -0.0807 0.3231 18.4853 -0.0000 -0.0000 -0.0000 1.0000
Orig:
francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -2.3092 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 26.4827 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 19.0338
talairach xfm : /usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 125.6908 0.0000 0.0000 1.0000 -101.5173 0.0000 -1.0000 0.0000 147.0338 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 125.6908 -0.0000 0.0000 -1.0000 147.0338 -0.0000 1.0000 0.0000 101.5173 -0.0000 -0.0000 -0.0000 1.0000
This is the raw T1 to which the regions are registered:
Volume information for sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz type: nii dimensions: 256 x 256 x 192 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -96.0, zend: 96.0 TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.0069, y_r = -0.0360, z_r = -0.9993, c_r = -2.3092 : x_a = -0.9823, y_a = 0.1874, z_a = -0.0000, c_a = 26.4827 : x_s = -0.1873, y_s = -0.9816, z_s = 0.0366, c_s = 19.0338 Orientation : PIL Primary Slice Direction: sagittal
voxel to ras transform: -0.0069 -0.0360 -0.9993 99.1125 -0.9823 0.1874 -0.0000 128.2306 -0.1873 -0.9816 0.0366 165.1330 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -0.0069 -0.9823 -0.1873 157.5619 -0.0360 0.1874 -0.9816 141.6386 -0.9993 0.0000 0.0366 92.9949 -0.0000 -0.0000 -0.0000 1.0000
Il giorno ven 22 feb 2019 alle ore 22:19 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
That looks right. Can you verify that the seg (sourcedata...) is in the conformed anatomical space? Use mri_info can compare the output (particularly the vox2ras matrix) against orig.mgz. If they are the same, you can try adding --invertmtx to the mri_label2vol command line.
On 2/22/19 2:24 PM, Francesca Strappini wrote:
External Email - Use CautionThanks a lot, Doug! I run the preprocessing: preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session And the runs look well registered.
Then I run mri_label2vol: mri_label2vol --seg /home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz --reg register.dof6.lta --temp template.nii.gz --o sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz
The region is in the correct space but completely misaligned. The misalignment is even bigger than the unregistered region. Maybe I'm not running the function correctly. This set of regions are in the same space of the functional data but registered to the raw T1.
Best Francesca
Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
There should be a registration file called register.dof6.lta. Use that with mri_label2vol passing your segmentation in with --seg. Run with --help to get more info
On 2/21/19 11:54 AM, Francesca Strappini wrote:
External Email - Use CautionThanks a lot! Running preproc-sess with the --per-session flag is exactly was I was looking for! Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were created outside freesurfer. These regions are in volume space and have the same resolution and box size of the functional runs. They are registered to the T1 that was used for the reconstruction of the surface. I've tried different functions for the registration but nothing really worked. I suppose I need a registration matrix that relates these regions to the reference image I used during the preprocessing and to apply this to each region. What's the best procedure?
Best Francesca
Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
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 CautionI'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 beimproved?
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 runmri_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 BruceFischl
> > <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 Strappiniwrote:
> > > > > > > > > > > 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 itdoable?
> > > > > > > > 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
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
You will need to either get the ROIs into the anatomical space or compute a new registration to the space of the ROIs from the functional template
On 2/22/19 3:43 PM, Francesca Strappini wrote:
External Email - Use Caution
Thanks! The vox2ras matrices are not same.
This is one region:
francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz type: nii dimensions: 64 x 64 x 50 voxel sizes: 3.000000, 3.000000, 3.000000 type: FLOAT (3) fov: 192.000 dof: 0 xstart: -96.0, xend: 96.0 ystart: -96.0, yend: 96.0 zstart: -75.0, zend: 75.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9988, y_r = 0.0235, z_r = 0.0427, c_r = -2.2923 : x_a = 0.0124, y_a = 0.9702, z_a = -0.2420, c_a = 19.4768 : x_s = 0.0471, y_s = 0.2412, z_s = 0.9693, c_s = 25.1269 Orientation : LAS Primary Slice Direction: axial
voxel to ras transform: -2.9964 0.0704 0.1281 88.1380 0.0373 2.9106 -0.7261 -56.7017 0.1414 0.7237 2.9080 -75.2534 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -27
ras to voxel transform: -0.3329 0.0041 0.0157 30.7614 0.0078 0.3234 0.0804 23.6988 0.0142 -0.0807 0.3231 18.4853 -0.0000 -0.0000 -0.0000 1.0000
Orig:
francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -2.3092 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 26.4827 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 19.0338
talairach xfm : /usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 125.6908 0.0000 0.0000 1.0000 -101.5173 0.0000 -1.0000 0.0000 147.0338 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 125.6908 -0.0000 0.0000 -1.0000 147.0338 -0.0000 1.0000 0.0000 101.5173 -0.0000 -0.0000 -0.0000 1.0000
This is the raw T1 to which the regions are registered:
Volume information for sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz type: nii dimensions: 256 x 256 x 192 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -96.0, zend: 96.0 TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.0069, y_r = -0.0360, z_r = -0.9993, c_r = -2.3092 : x_a = -0.9823, y_a = 0.1874, z_a = -0.0000, c_a = 26.4827 : x_s = -0.1873, y_s = -0.9816, z_s = 0.0366, c_s = 19.0338 Orientation : PIL Primary Slice Direction: sagittal
voxel to ras transform: -0.0069 -0.0360 -0.9993 99.1125 -0.9823 0.1874 -0.0000 128.2306 -0.1873 -0.9816 0.0366 165.1330 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -0.0069 -0.9823 -0.1873 157.5619 -0.0360 0.1874 -0.9816 141.6386 -0.9993 0.0000 0.0366 92.9949 -0.0000 -0.0000 -0.0000 1.0000
Il giorno ven 22 feb 2019 alle ore 22:19 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> ha scritto: That looks right. Can you verify that the seg (sourcedata...) is in the conformed anatomical space? Use mri_info can compare the output (particularly the vox2ras matrix) against orig.mgz. If they are the same, you can try adding --invertmtx to the mri_label2vol command line.
On 2/22/19 2:24 PM, Francesca Strappini wrote:
External Email - Use Caution
Thanks a lot, Doug! I run the preprocessing: preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session And the runs look well registered.
Then I run mri_label2vol: mri_label2vol --seg /home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz --reg register.dof6.lta --temp template.nii.gz --o sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz
The region is in the correct space but completely misaligned. The misalignment is even bigger than the unregistered region. Maybe I'm not running the function correctly. This set of regions are in the same space of the functional data but registered to the raw T1.
Best Francesca
Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> ha scritto: There should be a registration file called register.dof6.lta. Use that with mri_label2vol passing your segmentation in with --seg. Run with --help to get more info
On 2/21/19 11:54 AM, Francesca Strappini wrote:
External Email - Use Caution
Thanks a lot! Running preproc-sess with the --per-session flag is exactly was I was looking for! Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were created outside freesurfer. These regions are in volume space and have the same resolution and box size of the functional runs. They are registered to the T1 that was used for the reconstruction of the surface. I've tried different functions for the registration but nothing really worked. I suppose I need a registration matrix that relates these regions to the reference image I used during the preprocessing and to apply this to each region. What's the best procedure?
Best Francesca
Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> ha scritto: 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 CautionI'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.edumailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edumailto: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> <mailto: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>> <mailto: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>> <mailto: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>> > > <mailto: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>> > > <mailto: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>> > > <mailto: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>> <mailto: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>> > > <mailto: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 > > > _______________________________________________ > 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
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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.ilmailto: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.ilmailto: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.ilmailto:francesca.strappini@weizmann.ac.il
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What is the best procedure? I really have no idea, I've been tried so many things but nothing worked...
Il giorno ven 22 feb 2019 alle ore 23:41 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
You will need to either get the ROIs into the anatomical space or compute a new registration to the space of the ROIs from the functional template
On 2/22/19 3:43 PM, Francesca Strappini wrote:
External Email - Use CautionThanks! The vox2ras matrices are not same.
This is one region:
francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz type: nii dimensions: 64 x 64 x 50 voxel sizes: 3.000000, 3.000000, 3.000000 type: FLOAT (3) fov: 192.000 dof: 0 xstart: -96.0, xend: 96.0 ystart: -96.0, yend: 96.0 zstart: -75.0, zend: 75.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9988, y_r = 0.0235, z_r = 0.0427, c_r = -2.2923 : x_a = 0.0124, y_a = 0.9702, z_a = -0.2420, c_a = 19.4768 : x_s = 0.0471, y_s = 0.2412, z_s = 0.9693, c_s = 25.1269 Orientation : LAS Primary Slice Direction: axial
voxel to ras transform: -2.9964 0.0704 0.1281 88.1380 0.0373 2.9106 -0.7261 -56.7017 0.1414 0.7237 2.9080 -75.2534 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -27
ras to voxel transform: -0.3329 0.0041 0.0157 30.7614 0.0078 0.3234 0.0804 23.6988 0.0142 -0.0807 0.3231 18.4853 -0.0000 -0.0000 -0.0000 1.0000
Orig:
francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -2.3092 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 26.4827 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 19.0338
talairach xfm : /usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 125.6908 0.0000 0.0000 1.0000 -101.5173 0.0000 -1.0000 0.0000 147.0338 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 125.6908 -0.0000 0.0000 -1.0000 147.0338 -0.0000 1.0000 0.0000 101.5173 -0.0000 -0.0000 -0.0000 1.0000
This is the raw T1 to which the regions are registered:
Volume information for sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz type: nii dimensions: 256 x 256 x 192 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -96.0, zend: 96.0 TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.0069, y_r = -0.0360, z_r = -0.9993, c_r = -2.3092 : x_a = -0.9823, y_a = 0.1874, z_a = -0.0000, c_a = 26.4827 : x_s = -0.1873, y_s = -0.9816, z_s = 0.0366, c_s = 19.0338 Orientation : PIL Primary Slice Direction: sagittal
voxel to ras transform: -0.0069 -0.0360 -0.9993 99.1125 -0.9823 0.1874 -0.0000 128.2306 -0.1873 -0.9816 0.0366 165.1330 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -0.0069 -0.9823 -0.1873 157.5619 -0.0360 0.1874 -0.9816 141.6386 -0.9993 0.0000 0.0366 92.9949 -0.0000 -0.0000 -0.0000 1.0000
Il giorno ven 22 feb 2019 alle ore 22:19 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
That looks right. Can you verify that the seg (sourcedata...) is in the conformed anatomical space? Use mri_info can compare the output (particularly the vox2ras matrix) against orig.mgz. If they are the same, you can try adding --invertmtx to the mri_label2vol command line.
On 2/22/19 2:24 PM, Francesca Strappini wrote:
External Email - Use CautionThanks a lot, Doug! I run the preprocessing: preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session And the runs look well registered.
Then I run mri_label2vol: mri_label2vol --seg /home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz --reg register.dof6.lta --temp template.nii.gz --o sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz
The region is in the correct space but completely misaligned. The misalignment is even bigger than the unregistered region. Maybe I'm not running the function correctly. This set of regions are in the same space of the functional data but registered to the raw T1.
Best Francesca
Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
There should be a registration file called register.dof6.lta. Use that with mri_label2vol passing your segmentation in with --seg. Run with --help to get more info
On 2/21/19 11:54 AM, Francesca Strappini wrote:
External Email - Use CautionThanks a lot! Running preproc-sess with the --per-session flag is exactly was I was looking for! Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were created outside freesurfer. These regions are in volume space and have the same resolution and box size of the functional runs. They are registered to the T1 that was used for the reconstruction of the surface. I've tried different functions for the registration but nothing really worked. I suppose I need a registration matrix that relates these regions to the reference image I used during the preprocessing and to apply this to each region. What's the best procedure?
Best Francesca
Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
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 CautionI'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 beimproved?
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 runmri_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 ofmri_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 BruceFischl
> > <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 Strappiniwrote:
> > > > > > > > > > > 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 itdoable?
> > > > > > > > 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>
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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
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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
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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
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Hi Doug,
Sorry to bother, maybe my last message got lost. Do you think you can advice me on this type of registration? Thanks!
Best Francesca
On Fri, Feb 22, 2019, 11:44 PM Francesca Strappini < francescastrappini@gmail.com> wrote:
What is the best procedure? I really have no idea, I've been tried so many things but nothing worked...
Il giorno ven 22 feb 2019 alle ore 23:41 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
You will need to either get the ROIs into the anatomical space or compute a new registration to the space of the ROIs from the functional template
On 2/22/19 3:43 PM, Francesca Strappini wrote:
External Email - Use CautionThanks! The vox2ras matrices are not same.
This is one region:
francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz type: nii dimensions: 64 x 64 x 50 voxel sizes: 3.000000, 3.000000, 3.000000 type: FLOAT (3) fov: 192.000 dof: 0 xstart: -96.0, xend: 96.0 ystart: -96.0, yend: 96.0 zstart: -75.0, zend: 75.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9988, y_r = 0.0235, z_r = 0.0427, c_r = -2.2923 : x_a = 0.0124, y_a = 0.9702, z_a = -0.2420, c_a = 19.4768 : x_s = 0.0471, y_s = 0.2412, z_s = 0.9693, c_s = 25.1269 Orientation : LAS Primary Slice Direction: axial
voxel to ras transform: -2.9964 0.0704 0.1281 88.1380 0.0373 2.9106 -0.7261 -56.7017 0.1414 0.7237 2.9080 -75.2534 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -27
ras to voxel transform: -0.3329 0.0041 0.0157 30.7614 0.0078 0.3234 0.0804 23.6988 0.0142 -0.0807 0.3231 18.4853 -0.0000 -0.0000 -0.0000 1.0000
Orig:
francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -2.3092 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 26.4827 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 19.0338
talairach xfm : /usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 125.6908 0.0000 0.0000 1.0000 -101.5173 0.0000 -1.0000 0.0000 147.0338 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 125.6908 -0.0000 0.0000 -1.0000 147.0338 -0.0000 1.0000 0.0000 101.5173 -0.0000 -0.0000 -0.0000 1.0000
This is the raw T1 to which the regions are registered:
Volume information for sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz type: nii dimensions: 256 x 256 x 192 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -96.0, zend: 96.0 TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.0069, y_r = -0.0360, z_r = -0.9993, c_r = -2.3092 : x_a = -0.9823, y_a = 0.1874, z_a = -0.0000, c_a = 26.4827 : x_s = -0.1873, y_s = -0.9816, z_s = 0.0366, c_s = 19.0338 Orientation : PIL Primary Slice Direction: sagittal
voxel to ras transform: -0.0069 -0.0360 -0.9993 99.1125 -0.9823 0.1874 -0.0000 128.2306 -0.1873 -0.9816 0.0366 165.1330 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -0.0069 -0.9823 -0.1873 157.5619 -0.0360 0.1874 -0.9816 141.6386 -0.9993 0.0000 0.0366 92.9949 -0.0000 -0.0000 -0.0000 1.0000
Il giorno ven 22 feb 2019 alle ore 22:19 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
That looks right. Can you verify that the seg (sourcedata...) is in the conformed anatomical space? Use mri_info can compare the output (particularly the vox2ras matrix) against orig.mgz. If they are the same, you can try adding --invertmtx to the mri_label2vol command line.
On 2/22/19 2:24 PM, Francesca Strappini wrote:
External Email - Use CautionThanks a lot, Doug! I run the preprocessing: preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session And the runs look well registered.
Then I run mri_label2vol: mri_label2vol --seg /home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz --reg register.dof6.lta --temp template.nii.gz --o sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz
The region is in the correct space but completely misaligned. The misalignment is even bigger than the unregistered region. Maybe I'm not running the function correctly. This set of regions are in the same space of the functional data but registered to the raw T1.
Best Francesca
Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
There should be a registration file called register.dof6.lta. Use that with mri_label2vol passing your segmentation in with --seg. Run with --help to get more info
On 2/21/19 11:54 AM, Francesca Strappini wrote:
External Email - Use CautionThanks a lot! Running preproc-sess with the --per-session flag is exactly was I was looking for! Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were created outside freesurfer. These regions are in volume space and have the same resolution and box size of the functional runs. They are registered to the T1 that was used for the reconstruction of the surface. I've tried different functions for the registration but nothing really worked. I suppose I need a registration matrix that relates these regions to the reference image I used during the preprocessing and to apply this to each region. What's the best procedure?
Best Francesca
Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
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 CautionI'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 beimproved?
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, DouglasN.,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 runmri_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 ofmri_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 BruceFischl
> > <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 Strappiniwrote:
> > > > > > > > > > > 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 --movfunc_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 itdoable?
> > > > > > > > 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>
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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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Francesca Strappini -
Greve, Douglas N.,Ph.D.