Hi Martin, Thank you for your help.
By re-processing, do you mean running recon-alls all over again? Could you elaborate on the advantage of creating a new subjectsdir and copying over the orig dirs for each subject? On a related note, would it be better to run the full recon-all pipeline for each subject? I have been running batches of subjects at each stage (i.e. autorecon1, autorecon2, and finally autorecon3). Thank you again. Best Wishes, Elijah On Wed, Jan 15, 2014 at 9:02 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu>wrote: > Hi Elijah, > > if you have minimal edits, I'd recommend to reprocess the data from > scratch with 5.3 (that is supposed to be the same as using the -clean flag > when rerunning 5.3 on top of the old 5.0 data). But I'd recommend to create > a new subjectsdir, copy over the subjedid/mri/orig dirs for each subject > and rerun from scratch with 5.3 the independent, base and long runs. > > Best, Martin > > > > On 01/13/2014 06:18 PM, Elijah Mak wrote: > > Greetings Freesurfer Community, > > I am running a longitudinal study using Freesurfer v.5.3 to compare rate > of cortical thinning between 2 groups of subjects. I hope I can seek some > expert advice on the following situation: > > All data (both the baseline and follow-up) has been processed > independently using recon-all. This has been done on Freesurfer 5.0. > > Since then, I have upgraded to Freesurfer v5.3 to utilize the linear mixed > effect capability. > > For the construction of base and longs, I understand that it is important > to add -clean flag to my recon-all strings to overwrite brainmask.mgz etc. > When must this be done? > > I am still new to Freesurer, and I'd greatly appreciate any advice > regarding workflow. > > Many Thanks, > > Elijah > > > -- > > Elijah Mak, B.A. > > Doctoral Candidate *|* Psychiatry > > University of Cambridge *| *Department of Psychiatry > > Trinity College, Cambridge, CB2 1TQ > > > > > _______________________________________________ > 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 > > 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. > -- Elijah Mak, B.A. Doctoral Candidate *|* Psychiatry University of Cambridge *| *Department of Psychiatry Trinity College, Cambridge, CB2 1TQ
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