You can specify custom colors like this:

freeview -f lh.inlfated:overlay=xxx:overlay_custom=val,r,g,b,val2,r2,g2,b2 ...

val is the value of the color point, r, g, b are RGB values in the range of 0 to 255.

You can find more details from ‘freeview -h’.

Best, Ruopeng

On Feb 3, 2021, at 6:38 AM, Simone Cauzzo cauzzo.simone@gmail.com wrote:

    External Email - Use Caution        

Dear all, Using your precious hints in a past thread, I'm now displaying several surface analyses and taking a screenshot for each of them, everything from command line using the command freeview -f ***/mni152.fnirt/surf/lh.inflated:overlay=***mni152.fnirt.lh.nii.gz:overlay_threshold=5,8 -zoom 1.6 -ss ***.tif Now, the colormap I'm using is thus by default "heat" with thresholds 5 and 8. My images are very red. Opening the "configure overlay" menu in the GUI, I noticed that the colormap is almost entirely red, and fades to yellow only in the end. If I select "custom", the colormap appears more graded, as I would like it to be. Is there any way to specify the "custom" option in the "configure overlay" menu from the command line?

Thank you Simone _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer