Sorry, I believe I have fixed this by using --surface fsaverage lh. Thanks,
Kate On Fri, Mar 13, 2015 at 9:59 AM, Kate Riggall <kate.rigg...@gmail.com> wrote: > Bruce and Martin, > > Thanks, I now have it running of an external hard drive and it is working > well. As a follow-up question: > > When I run the paired analysis, the final command (mri_glmfit --glmdir > lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd > paired-diff.fsgd --C mean.mtx --C age.mtx) returns "ERROR: you must use > '--surface subject hemi' with surface data". I can add that flag easily, > but I am not sure what to put in the 'subject' spot, as I am looking at not > one subject but rather a large group. > > Also, given that I am running a two time point analysis, is it sufficient > to put the original subject names in the FSGD files, or should I specify > "subject.long" to use the longitudinally processed data? > > Cheers, > > Kate Riggall > > > On Thu, Mar 12, 2015 at 12:01 AM, Martin Reuter < > mreu...@nmr.mgh.harvard.edu> wrote: > >> Hi Kate, >> >> if you are only running stats on the longitudinally processed dirs, it >> should be sufficient to copy only the *.long.* directories and the base >> directories. You can skip the cross sectionals. >> >> If you do an LME, you can probably also skip the base dirs. But you'd >> need them for the 2-stage stats approach. >> >> Best, Martin >> >> >> On 03/10/2015 05:38 AM, Kate Riggall wrote: >> >> Hello, >> >> I am trying to run a paired analysis (a two time-point longitudinal >> analysis) on some subjects which have been longitudinally pre-processed for >> me on another computer. The computer I am now working on is originally a >> Windows computer, but is now running Linux on a partition (CentOS Release >> 6.6, Kernel Linux 2.6, GNOME 2.28.2). >> >> I have been advised by my IT staff to copy the files I need onto the >> linux partition to avoid any issues with accessing external/share drives. >> My subjects folder is 63 GB, which is a bit big to fit on the partition, so >> I am wondering if I can copy over just the files needed for the analysis >> step, and what those files would be. >> >> Thanks in advance, >> >> Kate Riggall >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Dr. Martin Reuter >> >> Instructor in Neurology >> Harvard Medical School >> Assistant in Neuroscience >> Dept. of Radiology, Massachusetts General Hospital >> Dept. of Neurology, Massachusetts General Hospital >> Research Affiliate >> Computer Science and Artificial Intelligence Lab, >> Dept. of Electrical Engineering and Computer Science, >> Massachusetts Institute of Technology >> >> 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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