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Ultrashort echo-time MRI as a substitute to CT for skull aberration correction in transcranial focused ultrasound: in vitro comparison on human calvaria


Clinical transcranial MR-guided focused ultrasound (TcMRgFUS) brain treatment systems compensate for skull-induced beam aberrations by adjusting the phase and amplitude of individual ultrasound transducer elements. These corrections are currently calculated based on a pre-acquired CT scan of the patient’s head. The purpose of the work presented here is to demonstrate the feasibility of using ultrashort echo-time (UTE) MRI instead of CT to calculate and apply aberration corrections on a clinical TcMRgFUS system.


Phantom experiments were performed in three ex vivo human skulls filled with tissue mimicking hydrogel. Each skull phantom was imaged with both CT and UTE MRI. The MR images were then segmented into “skull” and “not-skull” pixels using a computationally efficient, threshold-based algorithm, and the resulting three-dimensional binary skull map was converted into a series of two-dimensional virtual CT images. Each skull was mounted in the head transducer of a clinical TcMRgFUS system (ExAblate Neuro, Insightec, Israel), and transcranial sonications were performed using a power setting of approximately 750 Acoustic Watts at several different target locations within the electronic steering range of the transducer. Each target location was sonicated three times: once using aberration corrections calculated from the actual CT scan, once using corrections calculated from the MRI-derived virtual CT scan, and once without applying any aberration correction. MR thermometry was performed in conjunction with each 10-second sonication, and the highest single-pixel temperature rise and surrounding-pixel mean were recorded for each sonication.

Results and conclusions

Fig. 1 shows a UTE MR image and segmentation results from one of the skull phantoms. Fig. 2 shows a photograph of another skull phantom along with a 3D surface rendering generated from the binary bone map. The sonication results are summarized in Fig. 3. The measured temperature rises were ~45% larger for aberration-corrected sonications than for non-corrected sonications. This improvement was highly significant (p < 10–4). The difference between the single-pixel peak temperature rise and the surrounding pixel mean, which reflects the sharpness of the thermal focus, was also significantly larger for aberration-corrected sonications. There was no significant difference between the sonication results achieved using CT-based and MR-based aberration correction.

Figure 1
figure 1

Representative UTE MR image and segmentation results from skull #3. For imaging, the skull was immersed in a bucket of water. The segmentation algorithm assigned each image voxel to one of three classes: (1) air, (2) water/gelatin, (3) bone.

Figure 2
figure 2

Photograph of one of the skull phantoms (#2), and a 3D surface rendering generated from the MR-derived bone map.

Figure 3
figure 3

Graphical summary of sonication results. Each bar represents the average temperature rise of all sonications performed in all skulls using the same aberration correction method (none, CT-based, or MR-based).

Acknowledgements (Funding)

Jean-Francois Aubry is a consultant for the Focused Ultrasound Foundation.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

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Aubry, JF., Eames, M., Snell, J. et al. Ultrashort echo-time MRI as a substitute to CT for skull aberration correction in transcranial focused ultrasound: in vitro comparison on human calvaria. J Ther Ultrasound 3 (Suppl 1), P12 (2015).

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