Hi Rachele,
The automatic threshold setting of overlay in freeview was meant to just
quickly set an initial value for user to see. As I check the code, the high
threshold is set as the maximum value, the low is set simply as the mid point
between min and max values. It wasn’t meant to be
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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
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:
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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
