Hi Susan, I've updated that web page to demonstrate how to run the
random effects analysis. Let me know if that is clear or not.
doug
On 08/23/2012 12:38 PM, Susan Alice McLaughlin wrote:
Hi,
I'm resending this e-mail, as it didn't seem to go through correctly
yesterday:
I’m a Freesurfer novice, and I’m 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 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 as opposed to 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 analysis, 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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MGH-NMR Center
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