HI Rachele,
You can set overlay threshold from the command-line like this:
freeview -f lh.inflated:overlay=overlay_file:overlay_threshold=low,high
More information about threshold setting can be found by:
freeview -h
Best,
Ruopeng
On 3/10/20 11:29 AM, Rachele Sanfelici wrote:
External Email - Use Caution
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
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