[Freesurfer] overlay threshold in freeview

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Dear Freesurfer experts,

I created .mgh files from a dimensionality reduction analyses (similar to parcels from a known parcellation). These matrices have low values near to 0. When I overlay each of the .mgh file in freeview, it gets automatically thresholded with what seemed to me the median or mean of all the vertices' values (i.e., when looking at the "configure overlay" option)--however, this is not the case. Thus, I wanted to ask how the threshold is precisely set, so that I can automate and incorporate it in other scripts for binarizing my matrices.

Thanks a lot in advance for your help, Rachele