On Jan 15, 2026, at 11:33 AM, Camilo Castelblanco Riveros <camilo.a.castelblanco.riveros.gr@dartmouth.edu> wrote:
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_______________________________________________Hello Freesurfer Community,I’m visualising a surface overlay in Freeview (fsaverage inflated surface) using custom JSON colourmaps. For sequential features (mean/std), this works fine, but for signed significance-like maps, I want a diverging display with a “dead zone” around 0 (e.g., do not colour values between -2 and +2, so the underlying sulc/curv grey shading remains visible). With built-in colourmaps, Freeview can effectively truncate the middle, but with overlay_custom, the overlay always paints a colour (no alpha/transparent option), so I can’t keep the native curvature shading in the middle range.
Example command:
freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.inflated:annot=aparc.annot:annot_outline=1:overlay=/path/to/sig.mgh:overlay_custom="/path/to/custom.json" -viewport 3d -layout 1
Question: Is there a supported way in Freeview to make a value interval (e.g. [-2,2]) render as “no overlay/transparent” when using custom overlays, or is the intended workflow to pre-mask the overlay (e.g., set values in that interval to NaN) before loading?<image.png>
Thank you!
P.S. Is there a way to save images in vector format or PDF? The saving option hasn't allowed me===================================Camilo Castelblanco Riveros (He/His)Neuroscience Ph.D. Candidate (G4)Student Interest Group in Neurology (SIGN) Co-LeaderGlobal Health Fellow
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