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.
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
I will update my binaries and try it out.