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Hi,

I would like to replicate an analysis I did with qdec but regressing out  thickness at the vertex level. It’s a myelin group difference with age and left average myelin as nuisance factors.

Q1/ should I use smoothed thickness maps or unsmoothed?

I used the mri_glmfit command line generated during that qdec analysis and added the pvr flag but I got that error message:

ERROR: dimension mismatch between X and contrast 
/home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat
       X has 7 cols, C has 6 cols

I understood I had to change the contrast.mat and added a 0 at the end for the pvr: +1.00000 -1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 

Q2/ Can you please tell me if it is correct???

Many thanks,

Damien

fsgd:

GroupDescriptorFile 1
Title 10nov
MeasurementName R1projfrac0.5
Class group1
Class group2
Variables LH_mR1 Age 
Input suj1 group1 0.080687 1.644444
…

glm:
mri_glmfit --y /home/damien/bin/freesurfer6/subjects/qdec/10nov/y.mgh —fsgd /home/damien/bin/freesurfer6/subjects/qdec/10nov/qdec.fsgd dods --glmdir /home/damien/bin/freesurfer6/subjects/qdec/10nov --surf fsaverage lh —label /home/damien/bin/freesurfer6/subjects/fsaverage/label/lh.aparc.label --C /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat --C /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Diff-ct-dys-Intercept-R1projfrac0.5.mat --pvr lh.thicknessall.fsaverage.mgh