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Hi Doug,

This is the bulk of the text I wrote initially in my first email:

Dear experts,

I have recently tried to use the command line to examine thickness differences between two groups after controlling for the effects of age and sex. I get the following error :

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.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd CAA_CTRL_RH_Age_Sex.fsgd --C Contrasts/CAA-CTRL_Age_Sex.mtx --surf fsaverage rh --cortex --glmdir CAA_CTRL_RH_Age_Sex_Unix.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.000000 (col 5), Max=611.699463 (col 4) The scale is much different between columns 5 and 4, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 5, all values are 0 Column 6, all values are 0 Columns 5 and 6 are the same

I did not get this error when I was only looking at the difference in thickness between the two groups, so I am guessing there is not an issue with the file format? Looking at the log, does this mean that I also need to demean the age variable? I was planning on running some contrasts looking at the interactions between group and age after controlling for sex etc. in order to see if I should go with a DOSS approach, but using those contrasts still gives me the same error.

Thanks,

Arsenije

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Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subotic1@ucalgary.ca