Set zero color from command line

AFNI Message Board
1

Greetings!
Is there a way to set the zero color of the underlay image from the command line?
I am trying to automatically output jpegs of some axial slices in a script and want zero values to be a certain color.
Below is the command I am currently using.
afni -no_detach -com ‘OPEN_WINDOW A.axialimage’ -com ‘SWITCH_UNDERLAY input.nii.gz’ -com ‘SAVE_ALLJPEG A.axialimage output’ -com ‘QUITT’ .

Thank you for any help you may provide.

-Erika

2

Hi, Erika-

There is a snapshot-driving program in AFNI called “@chauffeur_afni”. If you have a very recent version of AFNI (say, AFNI_17.3.07), you should be able to see the help usage for it. It basically wraps around a lot of driving and environment-variable-setting functionality for AFNI, and you can make montage images in each of the major viewplanes with a single command. The zerocolor can be set using a command line option:


-zerocolor ZC      :Change the default 'background' ulay color of zero
                    values (def: "Black"); ZC can be set to any allowed
                    AFNI value (see ENV: AFNI_IMAGE_ZEROCOLOR).  This 
                    option is mainly for G. Chen, who flaunts convention
                    whenever possible.

–pt

3

Thank you!
I will update my binaries and try it out.
-Erika