freeview overlay_custom: how to create a transparent/“no overlay” band around 0 for diverging maps?
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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: 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)
Robertson Lab https://secure-web.cisco.com/11IId-FSIj2OB9o07kaQlCFuuH7EcJfRBMfniDZE2ADa-kEtg_ZLxdrmf9DIF3HdCUURsCQh468kXSBCB8Ft-IPkpu9XnUqzwxLXoDESAB-t-SBRvggdXQpnMsBSfFk0ZiWVe3IiJKBNmzkn3makF5auARrA8K2j5UucvIfjzkCvr_1N5VOzvmxW4R2kViRU_P38QQ8_v2m4Cbg2Kkj32lTFmoU7nFLlPcpEn1vtdGdn18ua76Tujo3S-w12HvqP-StuRRc4UByxm8HDL0p0WDWfjq_oeduPcpP81zEAAtVSYjjzxvCNdfB-8ILDW7TZj/https%3A%2F%2Fwww.robertsonlab.com%2F & Bujarski Lab https://secure-web.cisco.com/1dyd3QN20M10b3cHLFbP2mCJe0t7Zk0cwZJ25BnaffnKVn_ATTPrOTGvtsHoCK5i0pZoSh3YmGgD3C5mnEmwcKR_M_OF9XuhN_hSZ-HJWKlWPtx0G-yGdacNQUKCuUnbjRxcQvlTu9s5WHxreVpskJktO88P5R-ZP0gs8d4pKiacFyulwXzEzO11Ns5Ce07y9MZZuGZafVzzKUXcimS3QiOp8MCFykGkwNhFN4GB2y91rYC22jOsBaDqJK5WJI2w8MAZDgRAvsYnO0MMUiK0SgaPNCTijoxn3XuGpNrArbAoWKsaz4OKxum6R-dGB-XL4/https%3A%2F%2Fwww.dartmouth-hitchcock.org%2Fresearch%2Fsearch-clinical-trials%2Ftrial%2FSTUDY02001606
Student Interest Group in Neurology (SIGN https://secure-web.cisco.com/1F4yBWY2i0PLHYagzW9cPA92DGKJvl4QglUz0VOM7rIVDdaxklUnf4iq1TlNudgN350bOhvGalmcnMz-Pm5RI40b7O0T1fl7A6K_AwAMFObDgING_9kTQU8UK1kbX_XDs_gZ-GGtmg25sav04I12tMvtHiVBRJclC0LLgeN3Z2GgiYWojh4j14B_3qIRk88u9koJJ51rj9pFWNiSdgun5DPA-VJjNQOGSUxuItw40bZB7Weeg2jRkTEi7sVnZKSjZV98Fo8ACuoVcWECCWmcdKlj6UwSFhlaAbvicjyjPM324dfZEA3NoHL-bXc1774h93UQ38fASxFgXFLSWB5Q7kQ/https%3A%2F%2Fgeiselmed.dartmouth.edu%2Fstudent-gov%2Fstudent-groups%2F) Co-Leader
Global Health Fellow
e: ccastelblanco.gr@dartmouth.edu
Currently freeview does not support transparency (alpha channel) in custom defined overlay colors. I will add support for this.
Ruopeng
On Jan 15, 2026, at 11:33 AM, Camilo Castelblanco Riveros <camilo.a.castelblanco.riveros.gr@dartmouth.edumailto:camilo.a.castelblanco.riveros.gr@dartmouth.edu> wrote:
External Email - Use Caution
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) Robertson Labhttps://secure-web.cisco.com/11IId-FSIj2OB9o07kaQlCFuuH7EcJfRBMfniDZE2ADa-kEtg_ZLxdrmf9DIF3HdCUURsCQh468kXSBCB8Ft-IPkpu9XnUqzwxLXoDESAB-t-SBRvggdXQpnMsBSfFk0ZiWVe3IiJKBNmzkn3makF5auARrA8K2j5UucvIfjzkCvr_1N5VOzvmxW4R2kViRU_P38QQ8_v2m4Cbg2Kkj32lTFmoU7nFLlPcpEn1vtdGdn18ua76Tujo3S-w12HvqP-StuRRc4UByxm8HDL0p0WDWfjq_oeduPcpP81zEAAtVSYjjzxvCNdfB-8ILDW7TZj/https%3A%2F%2Fwww.robertsonlab.com%2F & Bujarski Labhttps://secure-web.cisco.com/1dyd3QN20M10b3cHLFbP2mCJe0t7Zk0cwZJ25BnaffnKVn_ATTPrOTGvtsHoCK5i0pZoSh3YmGgD3C5mnEmwcKR_M_OF9XuhN_hSZ-HJWKlWPtx0G-yGdacNQUKCuUnbjRxcQvlTu9s5WHxreVpskJktO88P5R-ZP0gs8d4pKiacFyulwXzEzO11Ns5Ce07y9MZZuGZafVzzKUXcimS3QiOp8MCFykGkwNhFN4GB2y91rYC22jOsBaDqJK5WJI2w8MAZDgRAvsYnO0MMUiK0SgaPNCTijoxn3XuGpNrArbAoWKsaz4OKxum6R-dGB-XL4/https%3A%2F%2Fwww.dartmouth-hitchcock.org%2Fresearch%2Fsearch-clinical-trials%2Ftrial%2FSTUDY02001606 Student Interest Group in Neurology (SIGNhttps://secure-web.cisco.com/1F4yBWY2i0PLHYagzW9cPA92DGKJvl4QglUz0VOM7rIVDdaxklUnf4iq1TlNudgN350bOhvGalmcnMz-Pm5RI40b7O0T1fl7A6K_AwAMFObDgING_9kTQU8UK1kbX_XDs_gZ-GGtmg25sav04I12tMvtHiVBRJclC0LLgeN3Z2GgiYWojh4j14B_3qIRk88u9koJJ51rj9pFWNiSdgun5DPA-VJjNQOGSUxuItw40bZB7Weeg2jRkTEi7sVnZKSjZV98Fo8ACuoVcWECCWmcdKlj6UwSFhlaAbvicjyjPM324dfZEA3NoHL-bXc1774h93UQ38fASxFgXFLSWB5Q7kQ/https%3A%2F%2Fgeiselmed.dartmouth.edu%2Fstudent-gov%2Fstudent-groups%2F) Co-Leader Global Health Fellow e: ccastelblanco.gr@dartmouth.edumailto:ccastelblanco.gr@dartmouth.edu Zoomhttps://secure-web.cisco.com/1TpnrTMiSXuR0AZwK-n65X5F9L-iGGIlwdoOm1tvaFTtsGc0P7e5DrnNlRNW-eLmlcnonOGvu9MuFyS7FWuC-_QoLxoT5UaSUD5gbS_T_36Fx-kaAlYyPXQn-PIpfccxC-VubGOVwBjYJx19k_bssmbKjUyVJ6QmVjYf65t3tbLb8MCcxlMavm6OcsVpK1OoBv0Y3BKHycKvUxzl_T3GQjhRDXA_PwwXrIh-_-_ZfUFjGQPIqphuiM4zqq-iPn2_GqRWsYcu2kmJce2fySPgEyaeJapbDl1Yi98niT3fKG3sr0K1kLYLRviluwAtTeLCzC93SvgB1VhahKzWO2fRPiA/https%3A%2F%2Fdartmouth.zoom.us%2Fmy%2Fccastelblanco [https://secure-web.cisco.com/17fwZ3Beq8naP8a12N1iv0yFSwoArm1xMGAFbYRptH99YIh...]
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Camilo Castelblanco Riveros -
Wang, Ruopeng