Back in June I shared the story of some headaches caused by inconsistent indexing: R (oro.nifti) and MRIcroN are 1-based, while python is 0-based. I later added SPM (1-based) and afni (0-based) to the collection; now, a kind person contributed images from doing the same test in FSL and caret: they are both 0-based.
As the person who sent the images wrote (I'm assuming wryly), ".... 'proper' programming languages (python, C) start counting/indexing from 0, while maths based applications like R and Matlab start from 1."
In FSL, the voxel at 17,15,20 is number 13 (0-based, like afni and pyMVPA), with voxel 25 at 18,16,21 (click images to enlarge).
And the same (0-based) is the case in caret, as shown in these images: