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In the Freeview 3.0 "Run Command" window, searching commands in the -h list, there are many ways to control image coloring. But I do not see anything for the "Clear background" capability. This capability is there in the GUI. If I load, say, a T1.mgz, and brainmask.mgz on top, for the brainmask.mgz volume, below the GUI color settings Color map / Window / Level / Min / Max sliders there are 3 buttons, the middle of which is "Clear background". Can this be switched on in a command line call?
I ask because I would like to automate image generation where the within-mask tissue is normal grayscale, but the out-of-mask tissue is colored with a heat map, and this is nicely done when I can clear the brainmask background.
Thanks, Jonathan
I don’t think that option can be turned on from the command line. I’ll add support for it.
Ruopeng
On Mar 2, 2026, at 5:47 PM, Jonathan Power jdp9009@med.cornell.edu wrote:
External Email - Use Caution
In the Freeview 3.0 "Run Command" window, searching commands in the -h list, there are many ways to control image coloring. But I do not see anything for the "Clear background" capability. This capability is there in the GUI. If I load, say, a T1.mgz, and brainmask.mgz on top, for the brainmask.mgz volume, below the GUI color settings Color map / Window / Level / Min / Max sliders there are 3 buttons, the middle of which is "Clear background". Can this be switched on in a command line call?
I ask because I would like to automate image generation where the within-mask tissue is normal grayscale, but the out-of-mask tissue is colored with a heat map, and this is nicely done when I can clear the brainmask background.
Thanks, Jonathan _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
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Wang, Ruopeng