Dear. All.
Hi. How are you?
It might be a very naive question, but your advice is greatly appreciated!
I'm trying to register 2 T1s obtained from 1 subject on different days and then register the functional scans to their corresponding T1s (registering the functional scans to the same day's T1). By doing so, I expect to get everything into the same space.
(Each subject was scanned twice on two different days etc., day1 and day2)
After running mri_robust_register onto day2's T1 as targetting day1's T1, I get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run preproc-sess(that does registration as well) onto day2's functional scans.
Is there a way to make preproc-sess do register functional scans of day2 to v2to1.mgz(of day2 that's created by mri_robust_register), not the original 046.mgz?
The commands that I run are:
recon-all -s $SUBJECT -all
mri_robust_register --mov /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz --iscale --satit
preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force -fwhm 0
Please feel free to give me any advice!
Thank you very much.
Best, Ji Won
Hi Ji-Won,
Why not just input both T1s to recon-all it will motion correct and average and then all of your functionals will be registered to the same FS data?
hth d
On Thu, Mar 17, 2016 at 3:06 PM, Ji Won Bang kirstens03@gmail.com wrote:
Dear. All.
Hi. How are you?
It might be a very naive question, but your advice is greatly appreciated!
I'm trying to register 2 T1s obtained from 1 subject on different days and then register the functional scans to their corresponding T1s (registering the functional scans to the same day's T1). By doing so, I expect to get everything into the same space.
(Each subject was scanned twice on two different days etc., day1 and day2)
After running mri_robust_register onto day2's T1 as targetting day1's T1, I get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run preproc-sess(that does registration as well) onto day2's functional scans.
Is there a way to make preproc-sess do register functional scans of day2 to v2to1.mgz(of day2 that's created by mri_robust_register), not the original 046.mgz?
The commands that I run are:
recon-all -s $SUBJECT -all
mri_robust_register --mov /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz --iscale --satit
preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force -fwhm 0
Please feel free to give me any advice!
Thank you very much.
Best, Ji Won
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi,
when using recon-all for this, the right way would be to run both images through the longitudinal stream. This will create a mid-space template and map both time points to it. That space can also be used as target for the functional data. That way you stay unbiased.
Probably the potential processing bias is small for this kind of analysis, so you can also probably get away with using the first time point structural space for everything. I am not familiar with the preproc-sess command to give advice. But there are others on this list who know.
Best, Martin
On 03/17/2016 03:16 PM, dgw wrote:
Hi Ji-Won,
Why not just input both T1s to recon-all it will motion correct and average and then all of your functionals will be registered to the same FS data?
hth d
On Thu, Mar 17, 2016 at 3:06 PM, Ji Won Bang kirstens03@gmail.com wrote:
Dear. All.
Hi. How are you?
It might be a very naive question, but your advice is greatly appreciated!
I'm trying to register 2 T1s obtained from 1 subject on different days and then register the functional scans to their corresponding T1s (registering the functional scans to the same day's T1). By doing so, I expect to get everything into the same space.
(Each subject was scanned twice on two different days etc., day1 and day2)
After running mri_robust_register onto day2's T1 as targetting day1's T1, I get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run preproc-sess(that does registration as well) onto day2's functional scans.
Is there a way to make preproc-sess do register functional scans of day2 to v2to1.mgz(of day2 that's created by mri_robust_register), not the original 046.mgz?
The commands that I run are:
recon-all -s $SUBJECT -all
mri_robust_register --mov /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz --iscale --satit
preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force -fwhm 0
Please feel free to give me any advice!
Thank you very much.
Best, Ji Won
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you for your reply!
I'll take a look at the longitudinal stream tutorial.
Best, Ji Won
2016-03-17 15:56 GMT-04:00 Martin Reuter mreuter@nmr.mgh.harvard.edu:
Hi,
when using recon-all for this, the right way would be to run both images through the longitudinal stream. This will create a mid-space template and map both time points to it. That space can also be used as target for the functional data. That way you stay unbiased.
Probably the potential processing bias is small for this kind of analysis, so you can also probably get away with using the first time point structural space for everything. I am not familiar with the preproc-sess command to give advice. But there are others on this list who know.
Best, Martin
On 03/17/2016 03:16 PM, dgw wrote:
Hi Ji-Won,
Why not just input both T1s to recon-all it will motion correct and average and then all of your functionals will be registered to the same FS data?
hth d
On Thu, Mar 17, 2016 at 3:06 PM, Ji Won Bang kirstens03@gmail.com
wrote:
Dear. All.
Hi. How are you?
It might be a very naive question, but your advice is greatly
appreciated!
I'm trying to register 2 T1s obtained from 1 subject on different days
and
then register the functional scans to their corresponding T1s
(registering
the functional scans to the same day's T1). By doing so, I expect to get everything into the same space.
(Each subject was scanned twice on two different days etc., day1 and
day2)
After running mri_robust_register onto day2's T1 as targetting day1's
T1, I
get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run preproc-sess(that does registration as well) onto day2's functional
scans.
Is there a way to make preproc-sess do register functional scans of
day2 to
v2to1.mgz(of day2 that's created by mri_robust_register), not the
original
046.mgz?
The commands that I run are:
recon-all -s $SUBJECT -all
mri_robust_register --mov /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz
--iscale
--satit
preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run
-force
-fwhm 0
Please feel free to give me any advice!
Thank you very much.
Best, Ji Won
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you
in
error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi. Daniel.
How are you?
Thanks for your reply.
That should be another option for me!
Thanks, Ji Won
2016-03-17 15:16 GMT-04:00 dgw dgwakeman@gmail.com:
Hi Ji-Won,
Why not just input both T1s to recon-all it will motion correct and average and then all of your functionals will be registered to the same FS data?
hth d
On Thu, Mar 17, 2016 at 3:06 PM, Ji Won Bang kirstens03@gmail.com wrote:
Dear. All.
Hi. How are you?
It might be a very naive question, but your advice is greatly
appreciated!
I'm trying to register 2 T1s obtained from 1 subject on different days
and
then register the functional scans to their corresponding T1s
(registering
the functional scans to the same day's T1). By doing so, I expect to get everything into the same space.
(Each subject was scanned twice on two different days etc., day1 and
day2)
After running mri_robust_register onto day2's T1 as targetting day1's
T1, I
get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run preproc-sess(that does registration as well) onto day2's functional
scans.
Is there a way to make preproc-sess do register functional scans of day2
to
v2to1.mgz(of day2 that's created by mri_robust_register), not the
original
046.mgz?
The commands that I run are:
recon-all -s $SUBJECT -all
mri_robust_register --mov /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz
--iscale
--satit
preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force -fwhm 0
Please feel free to give me any advice!
Thank you very much.
Best, Ji Won
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you
in
error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
dgw -
Ji Won Bang -
Martin Reuter