Hi Elijah, Just create a link ln -s pathtofsaverage ./
Usually this is done during recon-all Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Elijah Mak <[email protected]> Date:06/04/2014 7:17 AM (GMT-05:00) To: Martin Reuter <[email protected]>,[email protected] Subject: Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans Hi Martin, We corresponded about the longitudinal pipeline earlier. Your help has been much appreciated. I am now at the stage where I am ready to perform QDEC analyses using the 2-stage method. In my Subject DIR, I have all the longs (Tp1 and 2) and their corresponding bases. However, when i run the following command long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR It says that fsaverage is missing. Can I simply copy the fsverage folder from the default Freesurfer "subjects" folder? Many thanks! Best Regards, Elijah On Wed, Jan 15, 2014 at 10:15 PM, Martin Reuter <[email protected]> wrote: > Hi Elijah, > > > On 01/15/2014 04:10 PM, Elijah Mak wrote: > > Hi Martin, > > Thank you for your help. > > By re-processing, do you mean running recon-alls all over again? > > > Yes. 5.0 is old and it is better to run everything with 5.3 from beginning > to end. If you have a lot of data or a lot of edits, you can try running > -base and -long in 5.3 and keep the independent (cross sectional) stuff in > 5.0, but I don't recommend mixing versions. > > > > Could you elaborate on the advantage of creating a new subjectsdir and > copying over the orig dirs for each subject? > > This way you keep a backup copy of your old 5.0 processed data (to lookup > edits etc). If you have a script that calls recon-all with the -i flag for > inputs, you don't need to copy the mri/orig dirs (it will grab the data from > the dicoms again). Copying the orig dirs and dropping -i will skip that > step. > > > 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). > > Yes, full pipeline (-all) on all subjects is what I usually do. You can run > individual steps and check intermediate results if you like, but I usually > run everything and check everything at the end. > > Best, Martin > > > > Thank you again. > > Best Wishes, > Elijah > > > > > On Wed, Jan 15, 2014 at 9:02 PM, Martin Reuter <[email protected]> > 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 list >> [email protected] >> https://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: >> [email protected] >> [email protected] >> 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 > > > > -- > 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: > [email protected] > [email protected] > Web : http://reuter.mit.edu -- Elijah Mak, Gates Scholar PhD Candidate | Psychiatry University of Cambridge | Department of Psychiatry Trinity College, Cambridge, CB2 1TQ
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