Thursday, October 11, 2012
It took a little longer to get to than I'd planned, but contained in this post is a first pass at a checklist for acquisition parameters that I think should be included in the methods section of fMRI papers. This draft is an attempt to expand and update the list that was given in the 2008 paper from Poldrack et al. (I have reproduced below the section on acquisition that appeared in that 2008 paper.) Here, I tried to focus on the bulk of fMRI experiments that use 1.5 to 3 T scanners with standard hardware today. I further assumed that you're reporting 2D multislice EPI or spiral scanning. Advanced and custom options, such as multiband EPI, 3D scans and 7 T, will have to be added down the road.
In an attempt to make it didactic I have included explanatory notes. I went verbose instead of shorthand on the assumption that many fMRI papers don't include a lot of experimental detail perhaps because the authors don't possess that level of knowledge. We might as well learn something new whilst satisfying our collective desire for better manuscripts, eh? So, I haven't even tried to determine a shorthand notation yet. As others have already commented, having a checklist is probably more useful in the near term and the idea of a shorthand is a secondary consideration that has most value only if/when a journal is attempting to curtail the length of methods sections. But I'll take a stab at a shorthand notation once the checklist has been refined in light of feedback.
I've sorted the parameters into Essential, Useful and Supplemental categories in terms of value to a reader of a typical fMRI paper. Within each category the parameters are loosely sorted by functional similarity. In the Essential category are parameters whose omission would challenge a reader's ability to comprehend the experiment. Thus, there are several acquisition options - sparse EPI for auditory stimulus delivery is one example - that appear under Essential even though they are rarely used. The assumption is that everyone would report all the Essential parameters, i.e. that a reviewer should be expected to fault a paper that doesn't contain all the Essential parameters (and a journal should be held accountable for not permitting inclusion of all Essential parameters in the published methods section rather than consigning them to supplemental material).