Il giorno 10 mar 2020, alle ore 16:44, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> ha scritto:

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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer