External Email - Use Caution
Hi,
I am still struggling to examine differences in thickness using the command line stream for my two groups after controlling for age and sex. I get the following error when running the command line:
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
My design matrix is: 1 -1 0 0 0 0 (Examining difference in thickness after controlling for effects of age and sex)
I’ve also attached the FSGD file that I’ve been using. Please let me know if there is something wrong with the file (although I have used a similar file without the covariates and did not have any issues).
Thanks! Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1@ucalgary.camailto:arsenije.subotic1@ucalgary.ca
Your FSGD file is incorrect in several ways. Under "variables" you have "Sex" and list "Male" and "Female". The variables must be numbers, not strings. The variables should also represent continuous quantities, not categories. To handle sex, you should have a total of 6 categories, the 3 that you have divided into male an female.
On 3/5/19 12:51 PM, Arsenije Subotic wrote:
External Email - Use Caution
Hi,
I am still struggling to examine differences in thickness using the command line stream for my two groups after controlling for age and sex. I get the following error when running the command line:
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:
- Your command line:
mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgdCAA_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
My design matrix is: 1 -1 0 0 0 0 (Examining difference in thickness after controlling for effects of age and sex)
I’ve also attached the FSGD file that I’ve been using. Please let me know if there is something wrong with the file (although I have used a similar file without the covariates and did not have any issues).
Thanks! Arsenije
*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 mailto:arsenije.subotic1@ucalgary.ca
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