Education, tips and tricks to help you conduct better fMRI experiments.
Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Wednesday, July 31, 2013

Shared MB-EPI data

This is cool, publicly available test-retest pilot data sets using MB-EPI and conventional EPI on the same subjects courtesy of Nathan Kline Institute:

What's available:

The acquisition protocols are available as PDFs via the links given in the release website (and copied here). I like that they restricted the acceleration (MB) factor to four. I also like that the 3 mm isotropic MB-EPI data acquired at TR=645 ms used full Fourier acquisition (no partial Fourier) and an echo spacing of 0.51 ms. The former may help with signal in deep brain regions as well as frontal and temporal lobes, while the latter avoids mechanical resonances in the range 0.6-0.8 ms on a Trio, and also keeps the phase encode distortion reasonable.

There are already studies coming out that use these data sets, such as this one by Liao et al (which is how I learned of their existence). I don't yet know which reconstruction version was used for these data sets, but those of you who are tinkering should be aware that the latest version from CMRR, version R009a, has significantly lower artifacts and less smoothing than prior versions:

MB-EPI using CMRR sequence version R008 on a Siemens Trio with 32ch coil. MB=6, 72 slices, TE=38 ms, 2 mm isotropic voxels.

MB-EPI using CMRR sequence version R009a on a Siemens Trio with 32ch coil. MB=6, 72 slices, TE=38 ms, 2 mm isotropic voxels.

The bubbles visible in the bottom image of a gel phantom are real. The other intensity variations are artifacts. In both images one can easily make out the receive field heterogeneity of the 32-channel head coil.

Note added post publication

From Dan Lurie (@dantekgeek): We’re also collecting/sharing data from 1000 subjects using the same sequences, plus deep phenotyping