Hi Martin,
Thank you for your help.
By re-processing, do you mean running recon-alls all over again?
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.
Could you elaborate on the advantage of creating a new subjectsdir and copying over the orig dirs for each subject?
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.
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 <mreuter@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
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-- 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: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.eduThe information in this e-mail is intended only for the person to whom it is
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--
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: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu