Did you read the error message? It says:
Variable 2 has character string Female
Variables should be continuous numbers
You have listed Gender and Race as strings, they have to be numbers (eg,
1, 2)
You probably want to have these be discrete variables instead of continuous
On 11/10/2021 6:20 PM, Zeng, Qi wrote:
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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.
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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
<dgr...@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 agegenderrace eTIV
Inputsub001_baseControl85FemaleWhite1350519
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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