I’m trying to edit the range of the intensity bar in the afni viewer. Specifically I’d like to raise the lower bound from 0 to 0.95, and keep the higher bound at 1. Thus far it seems it’s only possible to change the higher bound.
I read that the lower bound is automatically set at the minimum voxel value in the map. If I cannot change this, how can I remove all values less than 0.95 (not just setting them to 0) whilst maintaining the true values of those > 0.95 (i.e. not setting them all to the same value)?
Thanks for the help!
Found a solution, I just subtracted 0.95 from each voxel using 3dcalc and then set the upper bound to 0.05 with pos unchecked on the GUI
Re. colorbar and overlay:
Let’s say the max colorbar max value is set to “A” (and A>0): this could be the max value in the dset, the 95% percentile in the dset, or any number of your choosing (you unselect the ‘default’ one and type it yourself). Then, the possible values of the bottom of the colorbar are either “-A” (“Pos?” box is unchecked) or 0 (“Pos?” box is checked).
To have a lower bound that is not -A or 0, you can, indeed, use 3dcalc to offset things, and have an effectively arbitrary lower bound.
For the underlay (possibly a sidenote):
You can set the gray/white (or other) colorbar to go from [B, C], where the lowerbound B is not constrained to be 0 or -C. To set that, right click on the vertical grayscale cbar in the image panel, select the upper “Choose Display Range”, and put in 2 numbers; note, it will only change it for that image panel.
Also try setting the AFNI environment variable, AFNI_PBAR_THREE = YES. To try it out, use this to start afni:
See this previous post for some more info.