Hi all,

I have a question about controlling freeview from the command line.

I would like to overlay some z-score maps for individual subjects on the fsaverage inflated surface. I would like to use the 'color wheel' color scale setting and threshold the images between -1 and 1 standard deviations (for example).

Because I have a number of subjects, I was hoping to make this a bit easier using the command line. So far I use the command:

freeview --surface /opt/freesurfer/subjects/fsaverage/surf/lh.inflated:overlay=lh.overlay.mgh:edgethickness=0 --screenshot lh.overlay.png

But I can't figure out from 'freeview --help' how to control the color of the overlay and the thresholding levels.

Does anyone know if it is possible to control these options from the command line? Or an alternative approach, maybe using tksurfer or even slicer?

Best wishes Heath