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Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Wednesday, November 14, 2012

Review: Using a bias field map to improve motion correction of EPI time series

In a new paper entitled "Effects of image contrast on functional MRI image registration," Gonzalez-Castillo et al. evaluate the performance of motion correction (a.k.a. registration) following a pre-processing step that aims to remove the contrast imparted across images due to receive (and/or transmit) field heterogeneity. A bias field map is estimated from a target EPI, and this reference image is then used to normalize the other images in the time series. There are other aims in the paper, too: specifically, to evaluate the performance of image registration (EPI to EPI, or EPI to MP-RAGE anatomical) when the T1 contrast of time series EPIs is altered via the excitation RF flip angle. But in this post I am going to focus on the normalization part because it involves the RF receive field heterogeneity, and this instrumentally-induced contrast is of particular concern for exacerbating motion sensitivity in fMRI (as explained here).

Although others have compared prescan normalization between different array coils (see the references in this paper), this is the first paper I've seen that compares motion correction performance for EPI time series acquired with an array coil (a 16-channel array) to a single channel birdcage coil. Now, this isn't quite the straightforward comparison I might like - with the receive fields being the only difference - because in this instance the birdcage is also used to transmit the excitation RF pulses, making the transmission (Tx) field for the birdcage experiment more spatially heterogeneous than will be produced from the body RF coil that's used when acquiring with a receive-only array coil. Following? In other words, for the 16-channel array the receive (Rx) field heterogeneity is likely to dominate whereas for the birdcage coil the heterogeneities of both the transmit and receive fields are salient. Still, it's worth a look since the coil comparison highlights the issue of the scanner hardware's influence on EPI contrast, and on subsequent motion correction.