I spent a few years in the late 90's and early 00's working on fMRI and I've been stunned by many of the claims that appear to arise from it's use. What's being measured relates to blood flow changes that correlate with an input block paradigm, typically from a visual stimulus. This isn't brain activity in the electrical sense but rather which areas of the brain appear to regulate their blood flow in relation to the stimulus. The assumption being that these areas require more 'fuel' to support their increased neural activity in response to the stimulus. Or as I like to think of it, attempting to estimate your home electricity usage by monitoring your water bill. Doing so with MRI, a technology I've spent most of my adult life analysing the data from and still can best describe what it does as 'magical', adding another not insignificant level of complexity.

I'm know there is good science going on in this field, by people that understand the limitations of the techniques and the technologies. However, I worked with psychiatrists - a clinical discipline starved of quantitative measurements until fMRI - that would happily ignore statistically significant activation in the air around the subjects head whilst laying claim as to the importance of those in the frontal cortex. Seeing the visual cortex 'light up' in response to flashing chequerboards is one thing, isolating those areas of the brain responsible for 'forgiveness' is something quite different.

Of course the software has bugs, I personally know people who wrote the package in question and they are extremely smart and also very human. I doubt I've ever published a paper using software that wasn't bug ridden. That's why open source is such an important part of the process, laying bare every last detail of what was done and not just what felt worth mentioning in the paper. The medical imaging research community is particularly good at this with most of the industry software making source code available. The problem with fMRI is not the software.