Hello AFNI experts,
Long time reader; first time writer here. The research I’m involved with usually uses the -Clustsim option in 3dttest++ when obtaining whole brain results. However, after reading about ETAC and its benefits, we wanted to try using that option. We ran our typical 3dttest++ command but also added the following arguments:
-ETAC_blur 0 4
After running without any errors, we immediately noticed that the free 1D text files were not generated. However, since the other output files (.ETACmask and .ETACmaskALL) for positive and negative seemed to be generated and contained non-zero values, we decided to continue. In AFNI, the positive binary mask looked like one giant cluster of 17862 voxels, so we followed the instructions on this forum thread. We ran a command like this:
3dClusterize -ithr 0 -idat 0 -inset INPUT_ETAC_MASK
-NN 1 -1sided RIGHT_TAIL 0.5 -clust_nvox 5
However, this did not change anything. 3dhistog revealed that we still had one giant cluster of 17862 voxels in our output file. First, we double-checked our 3dttest++ command, removing -Clustsim (which we kept to compare results) and running ETAC only with no extra blurring (mostly to speed up our troubleshooting).
This did not change our output: No errors but also no text files and only one large cluster. It was at this point that a colleague suggested that we instead use the regular 3dttest++ results (which were outputted like normal) and run those through 3dClusterize with the binary ETAC mask as the 3dClusterize mask. To compare results, we could also go into AFNI and check out the uncorrected results at p < .01, k = 5. We ran the following 3dClusterize command:
-1sided RIGHT_TAIL p=.01
This command gave us in different results than using 3dClusterize on the ETAC mask, and these results had various clusters! However, the results actually included clusters that were larger than the uncorrected AFNI results, which, obviously, is not right. This is when I thought to reach out to you all. Another development occurred while writing this though: 3dClustsim recommended the argument p = .005 for a one-sided test while my colleague was trying to solve this puzzle himself, so he decided to plug that value in (with all other arguments in the last 3dClustsim command I listed kept the same). The 3dClustsim results, at that point, mirrored what was seen in AFNI at uncorrected p < .01 (aside from some clusters that seemingly fell outside of the binary mask).
I am sure we went wrong somewhere in this process or our thinking, as we just cannot figure out why our “solution” would be the solution. Also, I am just not sure where those free text files would be since they are not with any of the other output. I’m sorry if this ends up being some obvious mistake, and any help would be greatly appreciated!