Freesurfer Group-Level Analysis (mri glmfit)

The group-level (Random-Effects) analysis repeats the contrasts performed for individual subjects on a variance-weighted composite of all your subjects. This will identify voxels for which your contrast effects are consistent across all your participants. For the function MRI group analysis you will need to:

• Concatenate individuals into one file (isxconcat-sess)
• Do not smooth (already smoothed during first-level analysis)
• Run mri_glmfit using weighted least squares (WLS)
• Correct for multiple comparisons
• Perform the above in each space (lh, rh, and/or mni305)
• Correct for multiple comparisons
• Optionally merge into one volume space

Before you start

Ensure that your SUBJECTS_DIR variable is set to the working directory containing all your participants, and that the first-level analyses have been completed for all participants (using selxavg-3)

Concatenate (isxconcat-sess)

In your $SUBJECTS_DIR, there should be a subjects file containing the subjectID for each participant for which you had run selxavg-3. Assuming that the analysis directories in each participant's folder is called my_analysis ( mkanalysis-sess), and that the contrasts folder is called conditionA_vs_conditionB ( mkcontrast-sess), run the isxconcat-sess script as follows:

• Left Hemisphere
  • isxconcat-sess -sf subjects -analysis my_analysis.lh -contrast conditionA_vs_conditionB -o RFX
• Right Hemisphere
  • isxconcat-sess -sf subjects -analysis my_analysis.rh -contrast conditionA_vs_conditionB -o RFX