That did the trick, but I'm having trouble displaying the results. First issue is that I can't seem to load my average surface in tksurfer from the command line.I get the following:
tksurfer average rh inflated surfer: current subjects dir: /data/nelson/work/alex/freesurfer/subjects_twins surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/nelson/work/alex/freesurfer/subjects_twins ERROR: cound not stat /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1/COR-.info. Does it exist? mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgh, -1): could not open file zcat: /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz.gz: No such file or directory mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz, -1): read error surfer: ### Could not find anatomical header information. What I do instead is load a subject's surface and then click load > Surface, and select the average one. When I load the sigt file as an overlay, what should I specify as the registration matrix? Clicking "calculate identity matrix" seems to work, so I'm assuming this is ok? After doing this, I can visualize the SPM ok, but have trouble when I try to obtain scatterplots for a gven vertex. tksurfer closes and I get the error below.(I've tried specifying markers and colors in the FSGD but it doesn't seem to make a difference) I'm using recon-all-nmr,v 1.104 2005/09/07. gdfReadHeader: reading /data/nelson/work/alex/freesurfer/subjects_twins/stats/twin_qualcheck_fsgd.txt WARNING: Marker for class class_subj1 was invalid. WARNING: Color for class class_subj1 was invalid. WARNING: Marker for class class_subj2 was invalid. WARNING: Color for class class_subj2 was invalid. WARNING: Marker for class class_subj3 was invalid. WARNING: Color for class class_subj3 was invalid. WARNING: Marker for class class_subj4 was invalid. WARNING: Color for class class_subj4 was invalid. WARNING: Marker for class class_subj5 was invalid. WARNING: Color for class class_subj5 was invalid. surfer: dmin=0.8701, vno=132952, x=14.6850, y=-30.1178, z=47.7694 % surfer: curv=0.000000, fs=0.000000 % surfer: val=2.132707, val2=0.000000 % surfer: amp=2.132707, angle=0.000000 deg (0.000000) Thanks again, A Oh, I'm sorry. I see the problem now. When I said to create a class for each subject, I meant for each person, not for each FreeSurfer subject. So there should only be 5 classes, not 10. So do something like this: Class class_subj1 Class class_subj2 Class class_subj3 Class class_subj4 Class class_subj5 Variables Time Input time1_subj1 class_subj1 -1 Input time2_subj1 class_subj1 +1 ... doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: > 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
