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.