Percentile thresholding option for 3dmerge or 3dclust

AFNI Message Board
1

Hi AFNI Gurus!

I would like to make a resting state FC mask of the top 10% of correlations in a single subject using 3dClust or 3dMerge. In other words, I would like to use percentile thresholding instead of p-value thresholding. This can easily be visualized in the GUI by simply checking the “percentile threshold” box and placing the sliding threshold to 0.90. However, I am having trouble identifying how to do this with 3dClust or 3dMerge in the command line.

Is there an option or work around for this? Thanks!!

2

You can find the voxel value that corresponds to the top 10% with this:

3dBrickStat -percentile 90 1 90 mydset

Then use that voxel value as your threshold for the clustering.

3

Thank you! When I initially ran your command, the output was zero (ie 90.0 0.0). After reading a different thread I found that a solution to that problem is to add the -non-zero option. (ie 3dBrickStat -non-zero -percentile 90 1 90 mydset).

Lastly, on some datasets the threshold from 3dclusterize generated from the GUI save mask button is different or slightly off from the 3dBrickStat command. Is there an explanation for this?

4

There could be rounding issue or whether the threshold is inclusive or not. Try using a slightly higher or lower number to experiment.