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High resolution fMRI at NeuRA, Sydney

Best Practice
Schira, Mark, Ph.D. Neuroscience Research Australia • Australia

32-channel head coil facilitates high resolution fMRI

Neuroscience Research Australia (NeuRA, Sydney) installed their first 3.0T magnet in 2003. MR scanning at NeuRA focuses mainly on the brain, including mood and aging disorders, brain injuries and general neuroscience research. High resolution fMRI has become much faster and easier since NeuRA received its 32-channel SENSE Head coil.
 Mark Schira, PhD NeuRA Imaging Center, Sydney, Australia
Mark Schira, PhD
NeuRA Imaging Center, Sydney, Australia

fMRI benefits from high resolution

Mark Schira, PhD, senior research officer at NeuRA, is using high-resolution fMRI to investigate the visual system, and perception in general. “We’re working on improving our techniques for retinotopic mapping and testing that our methods are valid,” he says. “In addition, we perform very high quality anatomical mapping of the brain, which would not be possible without the 32-channel coil.”

Dr. Schira’s high resolution fMRI looks at high detail organization of the visual cortex, showing how the different parts of the retina are mapped in the occipital lobes and how perception of contours
is organized. The visual cortex is well understood in neurosciences, and Dr. Schira says, “It’s still the gold standard for fMRI in general, and it’s a very useful system to work with if you’re interested in fMRI.” Paradigms for retinotopic mapping typically use a flickering checkerboard pattern, not shown at the complete visual field but restricted to a small part of the screen such as a wedge (a pie-slice that rotates around the circle) or rings growing out from the center. “We’re working on improving our techniques for retinotopic mapping. There’s a very tight control with respect to brain organization, and if a technique doesn’t quite work or has some issues, you will clearly see that because the data will not make any sense. The visual cortex is such a reliable system, it allows us to push the boundary and see whether we’ve been successful doing so.”

“We can see blood vessels in high resolution EPI scans. With typical EPI fMRI techniques using a 3 mm voxel resolution, we can’t see individual blood vessels, but beyond 1.5 mm, we can. High resolution fMRI is entirely necessary for that. The visualization of the blood vessels allows the researchers to make the distinction between ‘brain or vein.’ In other words, they can be sure that the BOLD signal response comes from the cortex and not from the down-stream venous system.”
 3 x 3 x 3 mm3 1.5 x 1.5 x 1.5 mm3 1 x 1 x 1 mm3
3 x 3 x 3 mm3
1.5 x 1.5 x 1.5 mm3
1 x 1 x 1 mm3

Example of EPI data from the same subject, at the standard resolution of 3 x 3 x 3 mm3, 1.5 x 1.5 x 1.5 mm3 resolution and 1 x 1 x 1 mm3 resolution, all measured with the 32-channel SENSE Head coil. The 1 mm scan would have not been possible with the 8-channel coil. The 1.5 mm protocol has become our bread and butter fMRI protocol for retinotopic mapping.
 3D SPAIR multiplanar reconstructions 3D SPAIR multiplanar reconstructions 3D SPAIR multiplanar reconstructions
3D SPAIR multiplanar reconstructions
3D SPAIR multiplanar reconstructions
3D SPAIR multiplanar reconstructions

High resolution T2-weighted scan (0.5 x 0.5 x 0.6 mm3) of a healthy volunteer. Purpose of this scan was to evaluate the level of quality achievable with the 32-channel SENSE Head coil. Note the fine detail in the cerebellum.

32-channel head coil provides higher resolution, quickly and easily

NeuRA received the 32-channel head coil at the end of 2010. “We managed to image the foveal confluence with the 8-channel head coil in 2009,” says Dr. Schira, “but repeating this work will be much easier with the 32-channel coil. It will be less noisy so we can do shorter scans, which is cheaper and easier on the subject. With the 8-channel coil, we sometimes scanned for 120 minutes to get enough SNR with the small voxels, but now with the 32-channel coil we can do it in about half of the time.”

The foveal confluence is an area of overlapping cortical regions which has been thought particularly difficult to disentangle. “It’s possible to do high resolution fMRI work with the 8-channel coil. It gave us 1.2 mm resolution when we were really pushing the coil,” says Dr. Schira. “Now, with the 32-channel coil, we get to 0.9 x 0.9 x 0.9 mm resolution, mostly because of the increased SNR, especially in the superficial parts of the cortex.”

“The difference between 1.2 mm and 0.9 mm may not sound that impressive,” he adds, “but when comparing it to fMRI resolution that others routinely do, between 2 mm and 4 mm, the difference is stunning. That’s where the 32-channel coil has really added value to our work.”

“The high resolution was easily obtained with the combination of Achieva 3.0T TX and the 32-channel SENSE Head coil,” says Dr. Schira. “The flexibility of the EPI protocols was really good, and it was easier to get to these high resolutions than with other scanning systems. High resolution fMRI on the Achieva 3.0T TX is incredibly simple and straightforward.”

Dr. Schira used SENSE factors of around 2.0-2.4 with the 8-channel coil, but was able to increase this to 3.5 or even 4.0 with the 32-channel coil. “The higher SENSE factor reduces geometric distortion of the scan, allows us to scan more slices in the same time and maintains the echo
time at the optimum for measuring the BOLD response.”

In addition to a remarkable 0.9 mm voxel size for fMRI, NeuRA’s researchers are not stopping in their quest for perfection. “We’re trying to improve the image quality of anatomical mapping, too.
We have acquired 0.6 mm T2 and T1 datasets. I don’t think that would have been possible without the 32-channel head coil,” says Dr Schira.

In the future, Dr. Schira hopes to see the availability of 3D EPI sequences. “This will allow us to use SENSE acceleration in more than one direction, to acquire multiple slices at the same time and have high resolution and larger coverage.”

Retinotopic mapping data projected onto a reconstructed and smoothed brain surface
(1.5 mm isotropic fMRI from a single volunteer, average of 3 x 5 minute scans). Purple and red lines demark the border between early visual areas. The circular legend depicts position in the visual field resulting in the strongest BOLD modulation.

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Jun 19, 2012

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Best Practice
Achieva 3.0T TX
32ch SENSE Head coil, fMRI, MultiTransmit, Neuro, visual cortex

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