Thanks so much, Doug! I got the same results for both of these contrast 
matrices, so my original question is all set.

However, I was surprised when I ran mri_glmfit-sim that there were 47 clusters 
for the LH, some as small as 2.51mm^2 (and the max 382.23mm^3, which is way 
smaller than what I found in qdec with the 2 group analysis of these data). So, 
I’m thinking this can’t be correct (particularly with 1.3 threshold).

I followed the steps here 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and copied 
my commands below.

1. mris_preproc
mris_preproc --fsgd dx4subgroups_n146.fsgd --cache-in 
thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out 
dx4subgroups_n146-lh-thickness.mgh


2. mri_glmfit
mri_glmfit --y dx4subgroups_n146-lh-thickness.mgh --fsgd dx4subgroups_n146.fsgd 
dods --C group.effect.mtx --surf fsaverage lh --glmdir 
dx4subgroups_n146-lh-thickness_Fmatrix.glmdir

3. mri_glmfit-sim
mri_glmfit-sim --glmdir dx4subgroups_n146-lh-thickness_Fmatrix.glmdir --cache 
1.3 abs --cwp  0.05 --2spaces

Do you see any issues?

Thank you so much for your help!

Best,
Andrea



Re: [Freesurfer] contrast matrix for one-way ANOVA with 1 factor, 4 
groups<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+contrast+matrix+for+one%5C-way+ANOVA+with+1+factor%2C+4+groups%22&o=newest>
Douglas N 
Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22>
 Tue, 21 Feb 2017 12:53:08 
-0800<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170221>
That four group test will yield the same exact result as

1 -1 0 0

1 0 -1 0

1 0 0 -1

so I think you are ok



From: "Gold, Andrea (NIH/NIMH) [F]" <andrea.g...@nih.gov>
Date: Tuesday, February 21, 2017 at 3:09 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: contrast matrix for one-way ANOVA with 1 factor, 4 groups

Hi,

I am trying to run a cortical thickness analysis comparing four groups – my 
goal is to conduct an omnibus F-test testing for any group differences. I have 
0 covariates/nuisance regressors.

This would be equivalent to the “Contrast 4 group.effect.mtx” in this page, for 
3 groups: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V

But, instead of 3 groups I have 4 groups.

I thought the contrast matrix for 4 groups F-test would be:
1 -1 0 0
0 1 -1 0
0 0 1 -1

But for 3 groups it is:
1 -1 0
1 0 -1


Would you please clarify the correct contrast matrix for this test in 
Freesurfer mri_glmfit?

Thank you!
Andrea

--
Andrea Gold, Ph.D.
Section on Development and Affective Neuroscience
National Institute of Mental Health
9000 Rockville Pike MSC 2670
Bldg. 15K
Bethesda, MD 20892
Phone: 301-402-6955
Fax: 301-402-2010
Email: andrea.g...@nih.gov


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