Sarah,
3dLME should work fine with any size of mask. Make sure you have the most recent version of AFNI before your run your new 3dLME script. Alternatively, you could just apply the mask using 3dcalc to the 3dLME output from your original script (with the whole-brain mask).
Gang
Edited 1 time(s). Last edit at 08/17/2021 12:04PM by Gang.