Agree with fluidcraft here. I don't want to discount the importance of numerical analysis, but the different preprocessing and analysis packages that I am perso

Agree with fluidcraft here. I don't want to discount the importance of numerical analysis, but the different preprocessing and analysis packages that I am personally aware of make substantively different decisions about how to proceed. For example, a psycho-physiological analysis, a connectivity analysis that tries to show how connectivity with a seed region changes in response to task condition, done in SPM will deconvolve the BOLD signal in the seed region to get at a purported neural signal, while in FSL, the condition regressor is convolved with haemodynamic response function. Both are "correct" in that in an ideal world you should get similar results doing either thing, but in the real world you very well may not. Similarly, different packages may make different assumptions about smoothness of brain regions in calculating whether the size of a cluster is significantly above zero. And even when you use the same software package, there are various things you might do differently, parameters you might set differently; even the order of certain operations maybe switched around. A classic example of that has to do with slice timing correction. Since fMRI slices are acquired at different times, a typical thing to do would be to interpolate the slices so that you can treat them as if they were acquired all at the same time. However, motion correction between volumes, in which subject motion is partially corrected by jiggling around each image until they maximally overlap each other, can be done before or after slice timing correction; but the consequences of that is that motion artifacts can propagate through volumes in different ways depending on the order you do it in; but neither order is definitely better, because it matters how much motion is a problem in the scans, and how long it takes to acquire a volume (e.g. tr 2 seconds), and so on.