Hi Susan, sorry for the delay. If you want to use a random fx model, then dont include any of the ffx options, so just

/mri_glmfit --y xrun/lh.cope1.mgh --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label/

doug

On 08/22/2012 07:21 PM, Susan Alice McLaughlin wrote:

Hi,

I’m a Freesurfer novice, and am confused about how to run a 3rd level cross-subject analysis on the surface using as input cross-run .gfeats from 10 subjects generated from a 2nd level analysis of fMRI data in FSL.

Following the directions posted at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I have sampled the .gfeat copes and varcopes into standard surface space, using /mris_preproc/.

I would then go on to perform a 3rd level surface based analysis as the instructions suggest, using:

/mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh --ffxdof 163 --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label/

However, I want to use a random effects rather than fixed effects analysis. How do I do this? I tried /--yrfxvar/ as opposed to /--yffxvar/ but it didn’t work. And if I’m going to display the map resulting from this analysi! s, do I need to correct for multiple comparisons?

Many thanks in advance,

Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington

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