Hi Freesurfer Experts,

I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format).

However, I am getting this error:

Normalized matrix condition is 1e+08
Design matrix ------------------
 0.000   1.000   0.000  -28915.199;
 0.000   1.000   0.000   194736.703;
 0.000   1.000   0.000  -184311.000;
 1.000   0.000   18489.000   0.000;
--------------------------------
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
--------------------------------
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 /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat
  2. The FSGD file (if using one)
  3. And the design matrix above
Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat

There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it?

Thank you!
Gabriella

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