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
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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Douglas N Greve -
Susan Alice McLaughlin