Wednesday, December 22, 2010

Resting state fMRI - part III

The story so far...

Finally, here is the third part of a three-part series of posts that have sought to determine a general protocol for resting state fMRI (rs-fMRI). In the first post I reviewed a paper by van Dijk et al. that showed that spatial and temporal resolution didn't make a huge difference to the way resting state networks could be detected using current methods (i.e. seed cross correlation or ICA).

In the second post I presented the results of some simple tests that aimed to determine what sort of spatial coverage could be attained with parameters in accordance with the conclusions of the van Dijk paper. Temporal SNR (TSNR) was used as a simple proxy for data quality. It was found that TSNR for 3.5 mm in-plane resolution was fairly consistent across a range of axial and axial-oblique slice orientations, as well as for sagittal slices.

One question remained, however: given the tolerance to a longish TR (compared to event-related fMRI) for detecting resting networks, would it be beneficial to acquire many thinner slices in a longer TR, or fewer thicker slices in a shorter TR? Following van Dijk et al. we wouldn't expect any huge penalty from extending the TR a bit, but there might be a gain of signal in regions suffering extensive dropout which would suggest that thinner slices might be useful.