Structural and Functional Mapping for Neurosurgery

Function mapping for neurosurgery refers to a series of projects on developing and refining functional MRI (fMRI) and diffusion MRI techniques to allow surgeons to see and better understand brain function (through blood flow and water diffusion) as well as anatomy to spare critical areas. More...

New: Talos I, Rubin D, Halle M, Musen M, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263. PMID: 18164666.

MRT Data Mining

This project involves the analysis, archiving, and dissemination of anonymized MRT scans for the validation of non-rigid registration algorithms as well as the retrospective analysis of these scans for the assessment of the utility of IGT technology. Already, as part of the dissemination efforts of the NCIGT, researchers have made available datasets of prostate and brain MRI scans. A broader part of this dissemination project is the establishment of a database of MRI data complete with schema and access documentation. For example, data will be viewable by demographics, pathologic results, predicted vs. observed complications, and calculations of success rate based on targeting the biopsy needle under MR-guidance that correlates with tumor volume measured on the MR images using Slicer. More...

New: Talos I, Archip N. Volumetric Non-Rigid Registration for MRI-Guided Brain Tumor Surgery. SPL brain tumor resection image dataset 2007 Aug;

Slicer Engineering

Slicer Engineering refers to a series of projects that focus on engineering and further refining and expanding 3D Slicer, the NCIGT's open source surgical navigation platform that has a developer-friendly modular design. Many projects are ongoing to further adapt Slicer to various IGT applications to keep pace with the IGT field and its needs. Two projects that relate to Slicer and that culminated in 2008 for dissemination to the public were brain and abdominal atlases for use with Slicer as surgical planning reference and teaching tools. Under Downloads, Slicer information along with other NCIGT resources can be found. More...

New: Ngo T, Westin C, Golland P. A White Matter Stochastic Tractography System. Int Conf Med Image Comput Comput Assist Interv. 2007;10(WS):94-104.

Blood Brain Barrier Disruption Via Focused Ultrasound

NCIGT researchers have shown the ability to move molecules using focused sound waves past the blood brain barrier (BBB), a protective vascular layer in the brain that shields the organ. Experiments using models and animals now focus on the effect of disruption particularly in regards to the degree of molecular penetration for cancer treatment agents, such as Herceptin or doxorubicin. Also being examined is the effect of multiple BBB treatments. More...

New: Treat L, McDannold N, Vykhodtseva N, Zhang Y, Tam K, Hynynen K. Targeted delivery of doxorubicin to the rat brain at therapeutic levels using MRI-guided focused ultrasound. Int J Cancer. 2007 Aug 15;121(4):901-7. PMID: 17437269.

Prostate Focused Ultrasound

Animal studies are being performed to test the effects of focused ultrasound on the prostate. Industrial partner Insightec, Inc, is providing the ultrasound device. Results from the study provide data on the device in preparation for US FDA review. As part of this work, researchers are assessing how models of thermal predictions compare to the measured temperatures obtained in the actual prostate during the focused ultrasound procedure. More...

New: Tempany C, Straus S, Hata N, Haker S. MR-guided prostate interventions. J Magn Reson Imaging, 2008 Feb;27(2):356-67. PMID: 18219689.

Prostate Imaging

Prostate imaging refers to several cross-core activities within the NCIGT to use MR image sequences to reduce needle artifact during prostate biopsy and to improve T2-weighted images and T2 mapping of the prostate to better carry out image guided therapy approaches such as seed placement in brachytherapy and the identification of targets for high intensity focused ultrasound ablation. Efforts are also underway to develop a temperature mapping protocol for focused ultrasound treatments of the prostate, including quantifying perfusion. More...

New: Zollei L, Jenkinson M, Timoner S, Wells W. A marginalized MAP approach and EM optimization for pair-wise registration. Inf Process Med Imaging. 2007;20:662-74. PMID: 17633738.

Advanced Focused Ultrasound Surgery Treatment Planning

Software is being planned to optimize treatment planning for MR-guided focused ultrasound treatments. Using a MR-compatible apparatus, researchers are performing planning and optimization on three tissue samples. The software will be used initially to guide treatment planning for MR-guided FUS for the brain, prostate, uterine fibroids, bone, and breast. More...

New: Farny C, Clement G. Feasibility of ultrasound phase contrast for heating localization. J Acoust Soc Am. 2008 Mar;123(3):1773-83. PMID: 18345865.

Real-Time Imaging Platform for MR Monitoring during Focused Ultrasound Treatments

A platform for guiding the delivery of energy and assessing the extent of resulting tissue damage is being designed to support minimally invasive focused ultrasound (FUS) treatment protocols. Requirements for such a platform include the ability to detect temperature changes, preferably in 3D and with a temporal resolution on the order of 1 second. Real time feedback in the form of temperature maps overlaid on anatomy is essential to insure that energy is delivered to the correct location and with sufficient intensity to ablate tumor tissue. More....

Panych L, Zhao L, Jolesz F, Mulkern R. Dynamic imaging with multiple resolutions along phase-encode and slice-select dimensions. Magn Reson Med. 2001 Jun;45(6):940-7. PMID: 11378870.

EPI Distortion Correction

Echo-planar imaging (EPI) distortion correction is project work aimed at assessing the impact of EPI distortion on fMRI analysis in the context of neurosurgical planning. Efforts led by the NCIGT's Computation Core involve the evaluation of the efficacy of current EPI distortion correction technology available in standard FMRI analysis software such as FSL and SPM. With at least 10 subjects, researchers are comparing the imaging results of EPI-to-structural registration with and without distortion correction. More

New: Zollei L, Shenton M, Wells W, Pohl K. The Impact of Atlas Formation Methods on Atlas-Guided Brain Segmentation. Int Conf Med Image Comput Comput Assist Interv. 2007;10(WS):39-46.

Toolbox to Support Enhanced MR Imaging in Image-Guided Therapy

A principal goal of the Imaging Core within the NCIGT is to develop freely available libraries of functions to support enhanced imaging in IGT. These are found on this site under Downloads. To this end, three separate but compatible libraries have been built containing:

• functions to support real-time data acquisition, reconstruction and scanner control
• functions to support enhanced imaging including the principal parallel imaging methods, temporal sampling methods such as UNFOLD and other reduced acquisition approaches
• functions to enable implementation of reduced field-of-view acquisition approaches by 2D RF selective excitation. More....

New: Hoge W, Kilmer M, Zacarias-Almarcha C, Brooks D. Fast Regularized Reconstruction of Non-uniformly Susbsampled Partial-Fourier Parallel MRI Data. Proceedings of the 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2007;4(1):1012-1015.

Improving Spatial Localization in MR Spectroscopic Imaging with PSF-Choice

This project's general aim is to exploit the advantages of RF encoding through the development of hybrid imaging sequences, combining RF encoding with Fourier-encoded MRI methods, and, to make these methods available as a resource for enhancing MRI-guided therapy applications. In a recent project, RF encoding is employed to improve spatial localization for MR spectroscopic imaging. More....

Panych L, Zhao L, Mulkern R. PSF-choice: a novel MRI method for shaping point-spread functions in phase-encoding dimensions. Magn Reson Med. 2005 Jul;54(1):159-68. PMID: 15968654.

K-space Energy Spectrum Analysis for Echo-Planar Imaging

The goal of this project is to improve the quality and spatial accuracy of echo-planar imaging (EPI) to derive accurate quantitative information from EPI-based medical research and clinical diagnosis. More....

New: Chen N, Oshio K, Panych L. Improved image reconstruction for partial Fourier gradient-echo echo-planar imaging (EPI). Magn Reson Med. 2008 Apr;59(4):916-24. PMID: 18383294.