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