External Email - Use Caution Dear Freesurfer experts,
Sorry for catching up so late, you can imagine the situation here in Europe.. Thank you Ruopeng for your answer! What I’m trying to figure out, though, is how Freeview automatically sets the threshold for overlays, not how to set it myself. I tried several combinations with my data (median, mean, 50th percentile), but none gives me the same result as the freeview automatic threshold. Could you please give me more information or a reference? Are you e.g. excluding the highest values (to avoid outliers) or truncating the values after e.g. 8 numbers after comma? Thank you again! > Il giorno 10 mar 2020, alle ore 16:44, Ruopeng Wang > <rpw...@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 > <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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 Rachele Sanfelici, Psychologin PRONIA Früherkennungsambulanz („Personalized Prognostic Tools for Early Psychosis Management“) Klinik und Poliklinik für Psychiatrie und Psychotherapie Ludwig-Maximilians-Universität München Nußbaumstr. 7, 80336 München Tel.: +49 (0)89/4400- 52731 Homepage: http://pronia.eu
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