Dear Blair,
you can run contrast manager in your batch to compute the necessary con/spmT images. You can also run a results report, but this would not write out thresholded files. Instead, you would have to feed the con or spmT images into ImCalc and do the thresholding based on t values there. If I remember correctly, contrast manager does not return dependencies for con/spmT images, thus I don't think this can be batched using dependencies right now.
Best,
Volkmar
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