align_epi_anat.py -epi_base max

Hello,

For the -epi_base parameter in align_epi_anat.py, there are the options of mean, median and max. My question is - max(/mean/median) of what? Is it the sub-brick with the maximal contrast? Or is it the maximum of something else?

Thanks,

Galit

These are voxelwise statistics across all TRs of the input EPI dataset as if you ran 3dTstat separately on the EPI dataset. The max is the maximum values across the EPI dataset.