Hi thank you for reply. May I ask other question; after editing the base it says to reocnstruct with recon-all -base -tp1 -tp2 etc. Does this require that all scans are located in the same directory? (Before i used symbolic links as scans are in different directories) but i am unsure whether after editing the abse anything further is actually done to the cross runs?
Thank you for your help, Anna On Tue, Feb 18, 2014 at 7:58 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu>wrote: > Hi Anna, > > the linear mixed effects models can include subjects with a single time > point and it would be a shame to drop that information. That is why we > modified the longitudinal pipeline (use 5.3) to allow processing of > subjects with a single time point. However, it is necessary that these > images undergo the same processing steps as the rest of the data (to avoid > bias). So you run it exactly as other subjects, with a cross sectional, > -base and a -long step: > > recon-all -all -s <tp1id> -i path_to_tp1_dcm > > recon-all -base <templateid> -tp <tp1id> -all > > recon-all -long <tp1id> <templateid> -all > > > Best, Martin > > > On 02/18/2014 04:58 AM, Anna Jonsson wrote: > > Dear Freesurfer experts, > > I want to know if possible when doing longitudinal stream to put subjects > with only one time-point through the processing (eg base and long runs) in > order to subsequently use with the Matlab lme tools? Or better is to leave > them out and only do those with 2+ times? > > Thank you > > Kind Regards, > > Anna > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Martin Reuter, Ph.D. > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreu...@nmr.mgh.harvard.edu > reu...@mit.edu > Web : http://reuter.mit.edu > > > _______________________________________________ > 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. > >
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