external p value dataset as threshold


We have used R and matlab for the decoding of trial-wise beta values. We’d now like to take our 3D stat maps and convert them to visualize in AFNI. We are able to write AFNI datasets and combine the stat files. Currently, as an example, we have a 3D dataset where sub-brick 1 is a t value, sub-brick 2 is a z value, and sub-brick 3 is a p value.

The issue is that we want to use the p value sub brick as a threshold. The threshold slider is from 0 to 1, however, since these are p values, we’d like it to be 1 to 0 so that we can threshold and only see voxels under a low p value threshold.

Perhaps this is a simple GUI option that I’m not familiar with to flip the polarity, or maybe there is a way add meta-data into the dataset to tell the GUI that these are p values?

Thank you,


Try setting AFNI_PBAR_THREE to YES or take the complement of your sub-brick with 3dcalc.

Dustin, most likely there are better options, but one way you can do is to artificially flip the sign of the p-value. Then you can threshold it the way you intend to do.

Thank you both! I’ll let you know if either of these don’t work.