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 <kirsten...@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
