Hi everyone, here I have another question of AFNI.
I want to create some masks in AFNI. In the GUI, using the coef sub-brick as overlay and the t stat map as threshold, it will display which voxels are significantly above a certain threshold (like p<0.0001).
My question is what command should I use to extract these voxels into a mask? I know 3dcalc -a XXX -expr ‘ispositive(a - certain values)’ can do the job of extracting voxels greater than certain values. But what if I want to make the ‘values’ here some p-values?
Just for anyone reading here to be aware, this question was also asked on the AFNI Message Board, and a (probably too lengthy) reply posted there:
A combination of p2dsetstat and 3dcalc can be applied, or 3dClusterize. Importantly, there are several considerations here of making sure that 2-sided p-to-stat conversions are done (rather than the often incorrectly done pair of uncorrected 1-sided thresholds); that the effect information isn’t lost (only looking at stats values); and that information loss due to the arbitrariness of thresholding can be mitigated using transparent thresholding.
