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]
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--
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
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