Hello from a new AFNI user!
Currently my lab is looking at fMRI activation during language tasks. Right now we look at statistically significant voxels using p values (p=0.05. 0.01, 0.001) that I change manually on the GUI after an overlay and underlay have been set. In the same GUI, how could I change the threshold to only show the top 10% of activated voxels?
There is a percentile thresholding check box in the Overlay panel. You could set that to 90%.
I see the percentile thresholding box but I do not see where I can input a value that I want.
Just raise the regular threshold slider to the point you want. The power of 10 control is ignored so that values from 0-1 on a power of 10 of 1 corresponds to 0-100%, and a power of 10 of 1 gives the same percentile range of 0-100. Likewise for all power of 10 values. Easier to try than to explain here.
would this be correct for top 10% activation?
Your image didn’t attach properly, but I think it’s relatively straightforward. You can use the Histogram plugin or 3dhistog to look at the distribution of your data. You could also use a command like this to find the threshold:
3dBrickStat -percentile 90 1 90 func_slim+orig’’
Also consider the functionality of 3dROImaker and some related scripts discussed here: