Okay, seriously, I'm tired of not being able to get overlay to work the way I expect. And I've been trying for something like, oh, 5 years.
I am overlaying a thresholded zstat volume on the MNI 2mm brain. Simple, yes? NO.
In the resulting overlaid volume, the MNI brain is red. I'd like it to be greyscale. The thresholded zstat volume is Red-Yellow, which is wonderful.
I am running this command:
overlay 1 0 $FSLDIR/data/standard/MNI152_T1_2mm_brain -a \
/tmp/cidx58_thr 0.000000 4.334596 \
Is there some switch that says, 'Be greyscale!'
I looked at the header information for the MNI brain and I don't see anything that specifies a LUT. The field 'aux_file' is blank.
Any suggestions are greatly appreciated as I have been battling this issue for years. Clearly I do not understand how overlay works.