AFNI Message Board

History of AFNI updates  

December 30, 2019 02:16PM
Hi there,

I know this topic has been covered before but I'm hoping for some help to make sure I understand all options for cluster thresholding after running 3dLME and/or 3dMVM.

So far, I have tried outputting the residuals then running:
3dFWHMx -ACF NULL -mask mask.nii -input residuals.nii -unif
3dClustSim -acf 0.34947 4.38785 11.4259 -mask mask.nii

(The mask is just a binary whole brain mask).

However, the resulting tables suggest that the clusters will need to be quite large to meet a corrected .05 threshold (k > ~90 voxels with uncorrected pthr=0.001). Two questions:

1. Outside of choosing an arbitrary cluster size threshold, is this the only/(correct?) way to threshold results by cluster extent from 3dLME/3dMVM? I looked at the etac slides but wasn't sure if there is a way to try this approach with results from 3dLME.

2. Do clusters this large seem reasonable or is there potentially an error in my approach? We lose a fair amount of activity in biologically interesting areas this way compared to a simple pthr=0.001, cluster k = 10 or 15 voxels.

Thank you for your help!
Subject Author Posted

Cluster thresholding after 3dLME

rwaugh December 30, 2019 02:16PM

Re: Cluster thresholding after 3dLME

Gang December 31, 2019 12:26PM

Re: Cluster thresholding after 3dLME

rwaugh December 31, 2019 01:21PM

Sorry, only registered users may post in this forum.

Click here to login