How to set the threshold value

AFNI Message Board
1

Hi all,

I’m trying to figure out how to set the threshold value of program 3dmerge, -1thresh.

E.g. 3dmerge -dxyz=1 -1clust 1 40 -1thresh 10.0 -prefix test_merged test.nii

Why use 10? Is this related to the # of voxels in a cluster?

Thank you,

Wan

2

Hi Wan,

That threshold is on the actual voxel values. For example,
it might be based on the t-stat for an uncorrected p-value,
while 40 is the voxel count and 1 is the radius.

What does test.nii contain? And forgetting any example,
exactly how do you want to threshold and cluster the data?

  • rick
3

Hi Rick,

The test.nii is the z value map of a hippo-cortical connectivity.

What I wanna do is to exclude the scattered and isolated voxels in my results. Is this make sense?

Thanks again,

Wan

4

Hi Wan,

The specific questions are what uncorrected z-value threshold
and what minimum cluster size do you want to apply? Exactly
what cluster limits do you want to impose?

  • rick