Hello Everyone,

I think I understand how the extent threshold is determined for a simple task-based voxelwise analysis. I find out the smoothness of the residual timeseries, feed that to the monte carlo simulation of noise done by 3dClustSim, which gives the extent thresholds at various uncorrected p-values to get the desired FWER. Correct me if I am wrong.

I need to know what is the way to determine the appropriate extent threshold for the following:

1. Connectivity analysis. I am using 3dGroupInstaCorr in the batch mode to put the seeds. Since no residual timeseries is generated, what to do? I could use the extent threshold from task-based analysis as a first guess. But how to justify its use? Is there a more appropriate way?
2. Contrast maps. I have two conditions in the experiment and I want to contrast the brain activation across them. What should be the appropriate extent threshold to apply to the contrast? Should I first subtract the residual of one condition from the other's, then use that difference timeseries as input to FWHMx and proceed as usual?
3. Contrast of connectivity maps. I have connectivity maps in two conditions and I want to contrast them. How to obtain the appropriate extent threshold?

I found this thread which was related to my questions but I didn't get an answer to how to find appropriate extent threshold
[afni.nimh.nih.gov]

This will be great help.
Thanks a lot!
Gaurav



Edited 1 time(s). Last edit at 03/23/2015 03:10PM by gauravm.