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The same tools (AFNI, SPM, and FSL) are used in a lot of other MR research protocols as well - not just fMRI.

They are but 3dClustSim (the culprit) is essentially used only for fMRI.

This is right and wrong: AFNI's 3dClustStim did contain a specific bug (since corrected) and is used for fMRI analysis, but the problem that the authors identified is more general than that and encompasses all of the tested packages.

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