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Hi Douglas, 

Here is the command line: 

mri_glmfit \

  --y rh.thickness-rate.MyStudy.10.mgh \

  --fsgd FSGD/MyStudy.fsgd dods\

  --C Contrasts/Case-Control_age_gender_race_etiv.mtx\

  --surf fsaverage rh \

  --cortex \

  --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \

  --eres-save

Also error message in terminal:

gdfRead(): reading FSGD/MyStudy.fsgd

WARNING: variable 1 is "Gender" which is often a discrete factor

  The proper way to handle discrete factors is to create classes.

  See MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples

ERROR: gdfReadV1: Format Error: Input line 1, subjid = sub001_base

 Variable 2 has character string Female

 Variables should be continuous numbers

FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input

Also attached FSGD file below. 

Thank you so much for the help!

Best, 

Zeng

On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

please send your command line and full terminal output as well as the fsgd file

On 11/10/2021 5:12 PM, Zeng, Qi wrote:

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Hi Freesurfer experts, 

Here, I want to design a simple group comparison (two levels: Case vs. Control) and also count for 4 covariates (two continuous and two categoricals). However, the GLM model cannot recognize my discrete variables. What do you suggest to change?

>> FSDG file:

GroupDescriptorFile 1

Title MyStudy

Class Control

Class Case

Variables age gender race  eTIV

Input sub001_base Control 85 Female White 1350519

Contrast:

>> Design matrix for Case-Control and regress out the effect of age, gender, race, and eTIV. 

-1 1 0 0 0 0 0 0 0 0 

Best, 

Zeng

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