External Email - Use Caution
Dear Freesurfer experts,
This is the first time I perform group analysis in Freesurfer. My aim is to compare the cortical thickness in four groups matched in age, sex and years of education using the Monte Carlo multiple comparisons correction. I tried to follow the Freesufer tutorials https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis to perform this group analysis and I would be really grateful whether someone can verify that all steps are correct. For example, for the cortical thickness (smooth = 15 FWHM) of the left hemisphere, the four steps that I followed were:
STEP 1. Assemble the cached Data (mris_preproc) using the fsgd file
mris_preproc --fsgd STUDY_4groups.fsgd \ --cache-in thickness.fwhm15.fsaverage \ --target fsaverage \ --hemi lh \ --out lh_J4G_thickness.15.mgh \
STEP 2. Perform a GLM Analysis (mri_glmfit)
mri_glmfit \ --y lh_J4G_thickness.15.mgh \ --fsgd STUDY_4groups.fsgd \ --C *group.effect.mtx* \ --surf fsaverage lh \ --cortex \ --glmdir left_hemisphere_thickness_results\
STEP 3. Perform Monte Carlo simulation
mri_glmfit-sim \ --glmdir left_hemisphere_thickness_results \ --sim mc-z 10000 4 mc-z.abs \ --sim-sign abs --cwpvalthresh 0.05\ --overwrite \
*QUESTIONS:*
1. Have I followed the steps to perform the analysis correctly or do you think I forgot some important flag?
2. Before test differences between two groups (eg. group1 > group 2 with the vector 1 -1 0 0) I would like to test any group effect. For that purpose, I created the group.effect.mtx contrast file (see below), is correct?
1 -1 0 0 0 1 -1 0 0 0 1 -1
Any help would be appreciated.
Best regards,
Steve
Yes, that is all correct. I only have a few comments. One is that 15mm is a lot of smoothing; this is not wrong, just more than the 5-10 that I usually use. Second, you might want to use permutation instead of MCZ; the threshold of 4 should make MCZ control the false positives adequately, but you might lose a lot of your activation.
On 10/21/2020 11:07 AM, Steve Petersen wrote:
External Email - Use Caution
Dear Freesurfer experts,
This is the first time I perform group analysis in Freesurfer. My aim is to compare the cortical thickness in four groups matched in age, sex and years of education using the Monte Carlo multiple comparisons correction. I tried to follow the Freesufer tutorials https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis to perform this group analysis and I would be really grateful whether someone can verify that all steps are correct. For example, for the cortical thickness (smooth = 15 FWHM) of the left hemisphere, the four steps that I followed were:
STEP 1. Assemble the cached Data (mris_preproc) using the fsgd file
mris_preproc --fsgd STUDY_4groups.fsgd \ --cache-in thickness.fwhm15.fsaverage \ --target fsaverage \ --hemi lh \ --out lh_J4G_thickness.15.mgh \
STEP 2. Perform a GLM Analysis (mri_glmfit)
mri_glmfit \ --y lh_J4G_thickness.15.mgh \ --fsgd STUDY_4groups.fsgd \ --C *group.effect.mtx* \ --surf fsaverage lh \ --cortex \ --glmdir left_hemisphere_thickness_results\
STEP 3. Perform Monte Carlo simulation
mri_glmfit-sim \ --glmdir left_hemisphere_thickness_results \ --sim mc-z 10000 4 mc-z.abs \ --sim-sign abs --cwpvalthresh 0.05\ --overwrite \
*QUESTIONS:*
- Have I followed the steps to perform the analysis correctly or do
you think I forgot some important flag?
- Before test differences between two groups (eg. group1 > group 2
with the vector 1 -1 0 0) I would like to test any group effect. For that purpose, I created the group.effect.mtx contrast file (see below), is correct? 1 -1 0 0 0 1 -1 0 0 0 1 -1
Any help would be appreciated.
Best regards,
Steve
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Douglas N. Greve -
Steve Petersen