do I need to run long_mris_slopes on the --qdec.long table?  the example is not for a longitudinal analysis. I have 2 time points and 3 groups. 



M. Alejandra Infante, Ph.D.
Postdoctoral Fellow
UC San Diego Department of Psychiatry
Adolescent Brain Cognitive Development (ABCD) Study
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreuter@nmr.mgh.harvard.edu]
Sent: Sunday, May 14, 2017 1:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] 2 stage model longitudinal data analysis

Hi Maria, 

yes, the example on the wiki is a simple “one sample group mean” (osgd). You can find examples with more than one group here:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples 

Best, Martin

On 13 May 2017, at 00:24, Maria A Infante <minfante@ucsd.edu> wrote:

Hi, 
I am interested in looking at groups differences (3 groups) in percent thickness change. I want to use mri_glmfit to analyze but I am unclear on what  I should include on my fsgd file. Can you please provide an example? 

Also The example provided on the fswiki  under Option mri_glmfit doesn't call for an fsgd file. 

long_mris_slopes --qdec long.testretest.qdec \
      --meas thickness \
      --hemi lh \
      --sd $SUBJECTS_DIR \
      --do-pc1 --do-label \
      --generic-time \
      --fwhm 15 \
      --qcache fsaverage \
      --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \
      --isec-labels lh.testretest.fsaverage.cortex.label

mri_glmfit --osgm \
           --glmdir lh.testretest.thickness-pc1.fwhm15 \
           --y lh.testretest.thickness-pc1.stack.fwhm15.mgh \
           --label lh.testretest.fsaverage.cortex.label \
           --surf fsaverage lh



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