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.
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).
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!