Hi all,
I have run the same image twice with recon-all and gotten different results for the cortical parcellation, with regions of the cortex differing an average of 2% in volume and the biggest difference being 11% (left bankssts). This is on a healthy, elderly brain. I'd like to try running images removing the random factor that apparently causes these differences. I found instructions on the internet to create an expert-options file to remove this random factor. I was wondering where this file should be saved. My problem is I am actually working remotely with parallel processing nodes, and I don't have permission to write to the freesurfer home directory. I was wondering, if I could use the whole path when I enter this command into recon-all, and then save it anywhere I like.
Thanks, Dana
Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003@med.cornell.edu
Dana, I believe you can achieve this by running recon-all on the subjects with the -norandomness flag. Unless you are using a version of FreeSurfer that is older than v3.0.4 - let me know if you are.
freesurfer@nmr.mgh.harvard.edu
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Allison Stevens -
Dana W. Moore