3dLME questions

Dear AFNI experts,

I am currenlty working on analyzing fMRI data using the 3dLME package. I stumbled upon 2 questions that I (as of now) could not find a satisfying answer to in the forum or through web search.

  1. Is it advisable to use a group-level mask (created by running a second level analysis in SPM) for a ‘whole-brain’ analysis? It seems more intuitive to me to use a mask here that includes only the voxels that are actually present for all subjects, in contrast to no masking (which is the default for 3dLME).

  2. How can I receive my alpha level for a cluster in the cluster report in AFNI (after manually putting in the voxel threshold from the 3dClustSim step in the gui)? Currently it says N/Csim in the Alpha column in the AFNI gui. I read that I may have to use 3drefit but I was unable to get it to work. Could you point me into the right direction? I am quite new to AFNI in general.

Please let me know if you need any more information.

Thanks in advance for your help!

Kind regards,


  1. A mask is useful for two reasons: (a) to hide the stuff outside the brain, and (b) provide FDR q-values in the output that would be unnecessarily penalized for the voxels outside the brain.

  2. The alpha level would be only available on the cluster report table if you perform the population-level analysis with 3dttest++. In your case with 3dLME, you have already decided the alpha threshold (presumably 0.05) through 3dClustSim. In other words, once you provide the cluster size threshold on the AFNI, all the surviving clusters would have an alpha level of 0.05 or less.