I still get the same error message. Maybe I've coded the variable wrong? gdfReadHeader: reading ./test_fsgd.txt INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) <= ncols (11)
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -----Original Message----- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 11:43 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Repeated-measures in mris_glm Yes, mris_preproc is new with stable. In your FSGD file, try specifying the title as a single string without spaces. doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: > Hi Doug, > Is mri_preproc a new addition to the stable version? I'm using > recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. > I tried running the analysis through mris_glm as per option 1 as you > described, but came across a problem. Command, error, and my FSGD are below. > Thanks, > Alex > > Command: > > mris_glm --surfmeas thickness --hemi lh --trgsubj ../average --fsgd > ./test_fsgd.txt doss --beta ./beta_doss_thickness-100_lh bfloat --var > ./var_doss_thickness-100_lh.w paint --y ./y_doss_thickness-100_lh_000.bfloat > --nsmooth 100 > gdfReadHeader: reading ./test_fsgd.txt > INFO: ignoring tag 1 > INFO: gd2mtx_method is doss > ERROR: Design Matrix: nrows (10) <= ncols (11) > > My FSGD: > > GroupDescriptorFile 1 > Title Time 1 vs Time 2 > Class class_time1_subj1 > Class class_time1_subj2 > Class class_time1_subj3 > Class class_time1_subj4 > Class class_time1_subj5 > Class class_time2_subj1 > Class class_time2_subj2 > Class class_time2_subj3 > Class class_time2_subj4 > Class class_time2_subj5 > Variables Time > Input time1_subj1 class_time1_subj1 -1 > Input time1_subj2 class_time1_subj2 -1 > Input time1_subj3 class_time1_subj3 -1 > Input time1_subj4 class_time1_subj4 -1 > Input time1_subj5 class_time1_subj5 -1 > Input time2_subj1 class_time2_subj1 1 > Input time2_subj2 class_time2_subj2 1 > Input time2_subj3 class_time2_subj3 1 > Input time2_subj4 class_time2_subj4 1 > Input time2_subj5 class_time2_subj5 1 > DefaultVariable Time > > Alex Fornito > M.Psych/PhD (clin. neuro.) candidate > Melbourne Neuropsychiatry Centre and Department of Psychology > National Neuroscience Facility > The University of Melbourne > Levels 2 & 3, Alan Gilbert Building > 161 Barry St > Carlton South Vic 3053 Australia > Ph: +61 3 8344 1624 > Fax: +61 3 9348 0469 > email: [EMAIL PROTECTED] > > > > -----Original Message----- > From: Doug Greve [mailto:[EMAIL PROTECTED] > Sent: Tue 4/11/2006 9:31 AM > To: Fornito, Alexander > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Repeated-measures in mris_glm > > > There are two ways to do it: > > 1. You can use DOSS, making each subject it's own class. Then create one > "Variable". For a given input, set the variable to either +1 or -1 > depending upon whether it corresponds to the first or second time > point. Then create a contrast as [0 0 0 0 ... 0 0 0 1], where there are > as many 0s as subjects. The last "1" will correspond to the Time Point > variable. > > 2. Alternatively, if you are using mris_preproc, you can specify > "--paired-diff", then just use a one-sample group mean test. See the > --help. This may be easier, and will also allow you to add a between > subject factor. > > doug > > > Fornito, Alexander wrote: > >> Hi, >> I'd like to run a simple repeated-measures analysis tetsing for change in >> thickness measures between 2 time points. There is no between-subjects >> factor, only the effect of time. Do I just set up a standard DOSS FSGD file, >> or do I use a different format? The tutorial only covers between-subjects >> designs. >> Thanks, >> Alex >> >> >> >> Alex Fornito >> M.Psych/PhD (clin. neuro.) candidate >> Melbourne Neuropsychiatry Centre and Department of Psychology >> National Neuroscience Facility >> The University of Melbourne >> Levels 2 & 3, Alan Gilbert Building >> 161 Barry St >> Carlton South Vic 3053 Australia >> Ph: +61 3 8344 1624 >> Fax: +61 3 9348 0469 >> email: [EMAIL PROTECTED] >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
