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:
External Email - Use Caution

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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.