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: alexander.fornito@wh.org.au
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] 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: alexander.fornito@wh.org.au
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] 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:
- 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.
- 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: alexander.fornito@wh.org.au
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