Custom color table is always continuous. So it will not automatically mask out a portion in the middle. The overlay_threshold option is not for custom colormap. I think we can add an option to allow specifying colors with 4 components where the last one is for alpha/transparency.

Ruopeng

On Oct 26, 2022, at 7:52 PM, Maya Yablonski <mayay@stanford.edu> wrote:

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Hello,

I'm trying to use a custom colormap for an overlay in Freeview and I can't get the threshold option to work. Specifically, I want to display positive values with specific colors, and negative values with different colors, similarly to using the threshold with the default Heat colorscale ('Hot' for positive and 'cold' for negative, values outside the threshold do not appear at all).

This is the code I've been using, and it seems to ignore the values provided by overlay_threshold:

freeview -f <MYPATH>/sub-01/surf/lh.inflated:overlay=<MYPATH>tmap.curv:overlay_custom=-3,45,0,130,-9,220,210,250,3,255,70,0,9,255,255,0:overlay_threshold=3,9:overlay_color='clearlower','clearhigher' -colorscale

This uses the right colors, but creates a continuous colorscale that spans -9 to 9, including the range [-3 3] which I want to threshold out of the map. I tried toggling the overlay_color='clearlower' and 'clearhigher', but couldn't find a combination that thresholded the low values around zero and not the extreme values (<-9 and >9). I also tested different values and seems like overlay_threshold is being completely ignored when overlay_custom is used. I couldn't get the right settings even when using the Freeview GUI.

I tested this on Freesurfer versions 7.1.1 and 7.3.2 on MacOS Catalina (10.15.7).
I'd appreciate any leads on this!

Thanks,

Maya
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