You can create your own color table file and put it in ‘luts’ folder under your FS home directory. There are a few stock color table files in that folder. You can copy and modify one of them to your own. The current color table does not support transparency, though. 

Ruopeng

On Jul 8, 2024, at 7:12 PM, Proulx, Jean Sebastien <JSPROULX@mgh.harvard.edu> wrote:

Hello,

This seems to be a longstanding issue, unless there is a post I miss.

How can one specify a custom colormap for a volume? Bonus point for how to specify an alpha channel for voxel-specific transparency.

My immediate goal: visualize angle data with a colorbar that wraps around a full circle (same color for values 0 and 2pi). That would be enough for now, but ultimately I want these angles to display with high transparency for voxels where the estimate is uncertain (low 2-d vector magnitude).

Thanks for the help and
Have a great day!
Sebastien
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer