that fixed the problem Thanks!!!! Jon ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, July 29, 2014 4:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec error

Try removing the mean from the age. By this I mean to compute the mean age over all subjects regardless of group, then subtract the mean from all ages. doug

On 07/29/2014 02:39 PM, Jon Alan Wieser wrote:

I'm getting the following erorr when running Qdec "Analyze"

Model Factors:

Discrete (fixed factors)

ADHD_Persist

MJ_group

Nuisance factor:

Age

ERROR: matrix is ill-conditioned or badly scaled, condno = 10355.4

Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.

If you seek help with this problem, make sure to send:

1. Your command line:

mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd

/Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir /Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label /Studies/MTA/fsaverage/label/rh.aparc.label --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd /Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir /Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label /Studies/MTA/fsaverage/label/rh.aparc.label --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat

command line:

mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCD/y.mgh --fsgd /Studies/MTA/qdec/MTA_persistanceCD/qdec.fsgd dods --glmdir /Studies/MTA/qdec/MTA_persistanceCD --surf fsaverage rh --label /Studies/MTA/fsaverage/label/rh.aparc.label --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Avg-Intercept-thickness.mat --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-C-D-Intercept-thickness.mat --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-Diff-Control-MJuser-Intercept-thickness.mat --C /Studies/MTA/qdec/MTA_persistanceCD/contrasts/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mat

no FSGD file

I have attached the qdec dat file

design matrix:

Design matrix ------------------ 1.000 0.000 0.000 0.000 25.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 22.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 25.000 0.000; 1.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 21.000 0.000; 0.000 1.000 0.000 0.000 0.000 25.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 23.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 26.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.000 0.000; 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 25.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 22.000 0.000; 1.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 21.000 0.000; 1.000 0.000 0.000 0.000 25.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000; 1.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.000 0.000; 1.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 26.000 0.000; 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 25.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.000 0.000; 1.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000; 1.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.000 0.000; 1.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 25.000 0.000; 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.000 0.000; 1.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 25.000; 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 25.000; 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 24.000; 0.000 1.000 0.000 0.000 0.000 22.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 27.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 26.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 24.000; 0.000 1.000 0.000 0.000 0.000 23.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 25.000; 0.000 1.000 0.000 0.000 0.000 26.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 25.000; 0.000 1.000 0.000 0.000 0.000 26.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 25.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 25.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 24.000; 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 26.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000;

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