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Hi Douglas,
If to set up the FSGD as below, is my design matrix for case and control comparison as "1 -1 1 -1 1 -1 1 -1 0 0" ?
GroupDescriptorFile 1 Title MyStudy Class CaseMaleWhite Class ControlMaleWhite Class CaseMaleNonWhite Class ControlMaleNonWhite Class CaseFemaleWhite Class ControlFemaleWhite Class CaseFemaleNonWhite Class ControlFemaleNonWhite Variables Age eTIV Input Sub001_base Control Female White 85 1350519.71 Input Sub002_base Control Female White 81.3 1558515.86
Best, Qi
On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I would advice setting up the FSGD files with 8 classes based on your 3 discrete, 2-level variables, eg, MaleControlWhite then use two continuous variables Age and eTIV. You should definitely normalize the eTIV (and probably age too)
On 11/10/2021 7:07 PM, Zeng, Qi wrote:
External Email - Use CautionHi Douglas,
Just to be clear, should I recode discrete variables as numeric as sample1) or change discrete variables into strings 2) or even change the comparison groups into strings too 3)?
Variables Age Gender Race eTIV Input Sub001_base Control 85 1 1 1350519.71 Input Sub002_base Control 81.3 0 1 1558515.86 Input Sub003_base Control 81.3 0 0 1558515.86
or 2) Variables Age Gender Race eTIV Input Sub001_base Control 85 "Female" "White" 1350519.71 Input Sub002_base Control 81.3 "Male" "White" 1558515.86 Input Sub003_base Control 72.7 "Male" "White" 1187649.47
or 3) Variables Age Gender Race eTIV Input Sub001_base "Control" 85 "Female" "White" 1350519.71 Input Sub002_base "Control" 81.3 "Male" "White" 1558515.86 Input Sub003_base "Control" 72.7 "Male" "White" 1187649.47
Best, Zeng
On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
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:
External Email - Use CautionHi 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://secure-web.cisco.com/1NEzix1p8cerzV2CscGJeOM5AxEOJi5zLORLiOeZ2wx-E6_... https://secure-web.cisco.com/1NHVxBIRnha6EjEdEho81-VE9d-vjJ6ivzt10z28vhX9c94pCwosQpkLG4Hfu3nLYp7KMDne5wAk9mK45YIQJEZBe6UlteF2wwLohmZJzp070UjHvv6fqugRAkgBk0uNO3Fsgo5BzblW95J5iO5sXWwZLK-LGAZJJTBaU7mLTkO5L70JRSscCW3pdc-G5KchZMbVyeY65gGH4w5MMIYBSVHvX03spMjZ85XkHbkgYYmWXTFnzqUGhqGgHygP5sLeR7OWPKIzEb7X3pHi7POf0UyEHJAZpQLU9bgT2BnOcClt0kW4mll1ODQDC2Y0U7-0f/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples 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 CautionHi 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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