Dear Atesh,
The conjunction principle as in Nichols et al. paper is that the minimum t value of all the contrasts will become the t value of the conjunction. Hence the correct method of doing conjunction is to do a random effects analysis and use the contrasts [1 0 0], [0 1 0] and [0 0 1] and do a conjunction between them. The alternative option is to do three one-sample t-tests, threshold them and do an imcalc to get a map where all the three overlap. if you want to know how much is the overlap, example in contrast A, the t-value may be 5 where as in contrast B, the t value may be 3. This you can do by using MRIcron or slover by projecting blobs of different colors e.g. red, blue, green and selecting the transparency of the colors, you can get the overlap areas using the usual RGB combinations. In general the Random effects analysis will be useful if you want to further probe into the results of your experiment such as finding the difference between contrasts A and B etc.
The other methods like implicit masking should not be used for conjunctions, because the t-value you get are from the main contrast selected. Masking only filters out voxels not active in the second contrast.
HTH
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