Neurosurgery Core

Alexandra Golby Lauren O'Donnell Nathalie Agar
Alexandra Golby, MD
Core Lead
Lauren O'Donnell, PhD
Project Lead
Nathalie Agar, PhD
Project Lead

The neurosurgery project is developing new technologies toward the long-term goal of allowing neurosurgeons in diverse settings to implement the advantages of image-guided therapy (IGT) for their patients. We investigate, develop, and validate approaches that address the two key problems in brain tumor surgery: to define the critical brain regions that must not be resected, and to define the extent and nature of the lesion. Put more simply, we create tools that support the neurosurgeon’s crucial decision of what to preserve, and what to remove. Maximizing tumor resection improves patients’ progression-free survival and overall survival; avoiding neurological deficits also improves survival and deeply impacts daily life for patients. Our strategies leverage preoperative and intraoperative imaging data to optimize brain tumor surgery. We are focusing on multimodality imaging data including diffusion MRI (dMRI), functional MRI (fMRI), and on applying mass spectrometry (MS) as a molecular analysis tool for tumor detection. To improve understanding of critical, individual patient brain functional anatomy, we jointly model functional and structural data for semi-automatic and improved localization of eloquent brain structures. To guide surgical decision making by better defining tumor margins, we investigate MS as an intraoperative molecular diagnostic method. Achievement of these goals supports the overall goal of NCIGT that is relevant for brain tumor surgery: to maximize the extent of tumor resection while minimizing the risk of neurologic deficit. Our projects are:

Computer-aided individualized labeling of critical brain structures. fMRI and dMRI provide pre-operative non-invasive maps of patients’ functional activations and white matter connections. fMRI and dMRI have been shown to increase resection and time of survival, but their translation to widespread clinical use faces significant challenges. Interpretation of the data is difficult, requiring extensive experience and time, and requiring software tools that are unwieldy and not clinically oriented. In order to provide more useful pre-operative mapping, we create a system that produces labeled maps of individual brain functional anatomy, even in cases with missing data, distortion, edema, or reorganization. Our overall strategy is to model the anatomical relationship between structural connections and functional activations, and to build models designed to generalize to patients with mass lesions or displacement, with the aid of machine learning algorithms. We are investigating the following novel and complementary tools: labeling of fMRI activations to produce a segmentation of a discrete set of cortical features of importance for neurosurgery, semi-automatic fMRI thresholding, multimodal calculation of language lateralization, and iterative joint labeling of fMRI activations and fiber tracts. We are developing the computational tools in stages so that each tool can be used either alone, or as part of the full system. We especially focus on the challenge of language mapping interpretation that requires identification of both the crucial language-specific functional cortical regions and the crucial language-specific fiber tracts. We are validating results using expert raters and intraoperative electrocortical stimulation data. Overall, we are creating the first image analysis software that can semi-automatically produce a multimodal structure-function map of individual patient anatomy for neurosurgery. (Contact: Lauren O'Donnell)

Optimal resection guided by mass spectrometry. Intraoperative decision making regarding how much tissue to resect during brain tumor surgery is of critical importance, yet as the surgery progresses the surgeon has access to less and less reliable data to guide this decision. To optimize the surgical resection of brain tumors, surgeons need more information to assess the boundaries between tumor and healthy tissue. In order to give surgeons a better understanding of the tissue being resected, we are investigating MS as an intra-operative molecular analysis tool for surgical guidance in the Advanced Multimodality Image Guided Operating Suite (AMIGO). The introduction of MS into routine surgical protocols for real-time characterization of tissue relies on the development and validation of the molecular reference system. The current iteration of the intraoperative platform is based on an ambient ionization methodology that allows for the analysis of tissue with little to no sample preparation. We validate the technology for real-time identification of surgical margins and molecular diagnosis by comparing against standard histopathology. The neurosurgeon stereotactically samples multiple specimens from each brain tumor resection and these are analyzed with a mass spectrometer in the AMIGO suite. We also correlate molecular, imaging and histopathologic findings in the 3D tumor space. Overall, our goal is to provide data equivalent or better to intraoperative MRI with less workflow disruption, less cost, and far less infrastructure needs. (Contact: Nathalie Agar)

Software and Documentation

3D Slicer, a comprehensive open source platform for medical image analysis, contains several modules that have been contributed by us for Image-Guided Brain Tumor Surgery. These include:
  • UKF Tractography Two-tensor modeling with Kalman filtering to track through regions of crossing and edema.

  • White Matter Analysis Software for modeling and segmentation of white matter tracts. The output is visualized in 3D Slicer.

  • Diffusion MRI in 3D Slicer Diffusion magnetic resonance imaging in 3D Slicer open-source software.



These presentations have been selected as tutorials for readers interested in learning about the clinical science and technology of the Neurosurgery Core.


Full Publication List

In NIH/NLM database and in our Abstracts Database.

Select Recent Publications

Essayed WI, Unadkat P, Hosny A, Frisken S, Rassi MS, Mukundan S, Weaver JC, Al-Mefty O, Golby AJ, Dunn IF. 3D Printing and Intraoperative Neuronavigation Tailoring for Skull Base Reconstruction after Extended Endoscopic Endonasal Surgery: Proof of Concept. J Neurosurg. 2018 :1-8.Abstract
OBJECTIVE Endoscopic endonasal approaches are increasingly performed for the surgical treatment of multiple skull base pathologies. Preventing postoperative CSF leaks remains a major challenge, particularly in extended approaches. In this study, the authors assessed the potential use of modern multimaterial 3D printing and neuronavigation to help model these extended defects and develop specifically tailored prostheses for reconstructive purposes. METHODS Extended endoscopic endonasal skull base approaches were performed on 3 human cadaveric heads. Preprocedure and intraprocedure CT scans were completed and were used to segment and design extended and tailored skull base models. Multimaterial models with different core/edge interfaces were 3D printed for implantation trials. A novel application of the intraoperative landmark acquisition method was used to transfer the navigation, helping to tailor the extended models. RESULTS Prostheses were created based on preoperative and intraoperative CT scans. The navigation transfer offered sufficiently accurate data to tailor the preprinted extended skull base defect prostheses. Successful implantation of the skull base prostheses was achieved in all specimens. The progressive flexibility gradient of the models' edges offered the best compromise for easy intranasal maneuverability, anchoring, and structural stability. Prostheses printed based on intraprocedure CT scans were accurate in shape but slightly undersized. CONCLUSIONS Preoperative 3D printing of patient-specific skull base models is achievable for extended endoscopic endonasal surgery. The careful spatial modeling and the use of a flexibility gradient in the design helped achieve the most stable reconstruction. Neuronavigation can help tailor preprinted prostheses.
Albi A, Meola A, Zhang F, Kahali P, Rigolo L, Tax CMW, Ciris PA, Essayed WI, Unadkat P, Norton I, et al. Image Registration to Compensate for EPI Distortion in Patients with Brain Tumors: An Evaluation of Tract-Specific Effects. J Neuroimaging. 2018;28 (2) :173-82.Abstract
BACKGROUND AND PURPOSE: Diffusion magnetic resonance imaging (dMRI) provides preoperative maps of neurosurgical patients' white matter tracts, but these maps suffer from echo-planar imaging (EPI) distortions caused by magnetic field inhomogeneities. In clinical neurosurgical planning, these distortions are generally not corrected and thus contribute to the uncertainty of fiber tracking. Multiple image processing pipelines have been proposed for image-registration-based EPI distortion correction in healthy subjects. In this article, we perform the first comparison of such pipelines in neurosurgical patient data. METHODS: Five pipelines were tested in a retrospective clinical dMRI dataset of 9 patients with brain tumors. Pipelines differed in the choice of fixed and moving images and the similarity metric for image registration. Distortions were measured in two important tracts for neurosurgery, the arcuate fasciculus and corticospinal tracts. RESULTS: Significant differences in distortion estimates were found across processing pipelines. The most successful pipeline used dMRI baseline and T2-weighted images as inputs for distortion correction. This pipeline gave the most consistent distortion estimates across image resolutions and brain hemispheres. CONCLUSIONS: Quantitative results of mean tract distortions on the order of 1-2 mm are in line with other recent studies, supporting the potential need for distortion correction in neurosurgical planning. Novel results include significantly higher distortion estimates in the tumor hemisphere and greater effect of image resolution choice on results in the tumor hemisphere. Overall, this study demonstrates possible pitfalls and indicates that care should be taken when implementing EPI distortion correction in clinical settings.
Zhang F, Wu W, Ning L, McAnulty G, Waber D, Gagoski B, Sarill K, Hamoda HM, Song Y, Cai W, et al. Suprathreshold Fiber Cluster Statistics: Leveraging White Matter Geometry to Enhance Tractography Statistical Analysis. Neuroimage. 2018;171 :341-54.Abstract
This work presents a suprathreshold fiber cluster (STFC) method that leverages the whole brain fiber geometry to enhance statistical group difference analyses. The proposed method consists of 1) a well-established study-specific data-driven tractography parcellation to obtain white matter tract parcels and 2) a newly proposed nonparametric, permutation-test-based STFC method to identify significant differences between study populations. The basic idea of our method is that a white matter parcel's neighborhood (nearby parcels with similar white matter anatomy) can support the parcel's statistical significance when correcting for multiple comparisons. We propose an adaptive parcel neighborhood strategy to allow suprathreshold fiber cluster formation that is robust to anatomically varying inter-parcel distances. The method is demonstrated by application to a multi-shell diffusion MRI dataset from 59 individuals, including 30 attention deficit hyperactivity disorder patients and 29 healthy controls. Evaluations are conducted using both synthetic and in-vivo data. The results indicate that the STFC method gives greater sensitivity in finding group differences in white matter tract parcels compared to several traditional multiple comparison correction methods.
Silva MA, See AP, Essayed WI, Golby AJ, Tie Y. Challenges and Techniques for Presurgical Brain Mapping with Functional MRI. Neuroimage Clin. 2017;17 :794-803.Abstract
Functional magnetic resonance imaging (fMRI) is increasingly used for preoperative counseling and planning, and intraoperative guidance for tumor resection in the eloquent cortex. Although there have been improvements in image resolution and artifact correction, there are still limitations of this modality. In this review, we discuss clinical fMRI's applications, limitations and potential solutions. These limitations depend on the following parameters: foundations of fMRI, physiologic effects of the disease, distinctions between clinical and research fMRI, and the design of the fMRI study. We also compare fMRI to other brain mapping modalities which should be considered as alternatives or adjuncts when appropriate, and discuss intraoperative use and validation of fMRI. These concepts direct the clinical application of fMRI in neurosurgical patients.
Zhang F, Savadjiev P, Cai W, Song Y, Rathi Y, Tunç B, Parker D, Kapur T, Schultz RT, Makris N, et al. Whole Brain White Matter Connectivity Analysis using Machine Learning: An Application to Autism. Neuroimage. 2018;172 :826-37.Abstract
In this paper, we propose an automated white matter connectivity analysis method for machine learning classification and characterization of white matter abnormality via identification of discriminative fiber tracts. The proposed method uses diffusion MRI tractography and a data-driven approach to find fiber clusters corresponding to subdivisions of the white matter anatomy. Features extracted from each fiber cluster describe its diffusion properties and are used for machine learning. The method is demonstrated by application to a pediatric neuroimaging dataset from 149 individuals, including 70 children with autism spectrum disorder (ASD) and 79 typically developing controls (TDC). A classification accuracy of 78.33% is achieved in this cross-validation study. We investigate the discriminative diffusion features based on a two-tensor fiber tracking model. We observe that the mean fractional anisotropy from the second tensor (associated with crossing fibers) is most affected in ASD. We also find that local along-tract (central cores and endpoint regions) differences between ASD and TDC are helpful in differentiating the two groups. These altered diffusion properties in ASD are associated with multiple robustly discriminative fiber clusters, which belong to several major white matter tracts including the corpus callosum, arcuate fasciculus, uncinate fasciculus and aslant tract; and the white matter structures related to the cerebellum, brain stem, and ventral diencephalon. These discriminative fiber clusters, a small part of the whole brain tractography, represent the white matter connections that could be most affected in ASD. Our results indicate the potential of a machine learning pipeline based on white matter fiber clustering.
Norton I, Essayed WI, Zhang F, Pujol S, Yarmarkovich A, Golby AJ, Kindlmann G, Wasserman D, Estepar RSJ, Rathi Y, et al. SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research. Cancer Res. 2017;77 (21) :e101-e103.Abstract
Diffusion MRI (dMRI) is the only noninvasive method for mapping white matter connections in the brain. We describe SlicerDMRI, a software suite that enables visualization and analysis of dMRI for neuroscientific studies and patient-specific anatomic assessment. SlicerDMRI has been successfully applied in multiple studies of the human brain in health and disease, and here, we especially focus on its cancer research applications. As an extension module of the 3D Slicer medical image computing platform, the SlicerDMRI suite enables dMRI analysis in a clinically relevant multimodal imaging workflow. Core SlicerDMRI functionality includes diffusion tensor estimation, white matter tractography with single and multi-fiber models, and dMRI quantification. SlicerDMRI supports clinical DICOM and research file formats, is open-source and cross-platform, and can be installed as an extension to 3D Slicer ( More information, videos, tutorials, and sample data are available at Cancer Res; 77(21); e101-3. ©2017 AACR.
Luo M, Frisken SF, Weis JA, Clements LW, Unadkat P, Thompson RC, Golby AJ, Miga MI. Retrospective Study Comparing Model-Based Deformation Correction to Intraoperative Magnetic Resonance Imaging for Image-Guided Neurosurgery. J Med Imaging (Bellingham). 2017;4 (3) :035003.Abstract
Brain shift during tumor resection compromises the spatial validity of registered preoperative imaging data that is critical to image-guided procedures. One current clinical solution to mitigate the effects is to reimage using intraoperative magnetic resonance (iMR) imaging. Although iMR has demonstrated benefits in accounting for preoperative-to-intraoperative tissue changes, its cost and encumbrance have limited its widespread adoption. While iMR will likely continue to be employed for challenging cases, a cost-effective model-based brain shift compensation strategy is desirable as a complementary technology for standard resections. We performed a retrospective study of [Formula: see text] tumor resection cases, comparing iMR measurements with intraoperative brain shift compensation predicted by our model-based strategy, driven by sparse intraoperative cortical surface data. For quantitative assessment, homologous subsurface targets near the tumors were selected on preoperative MR and iMR images. Once rigidly registered, intraoperative shift measurements were determined and subsequently compared to model-predicted counterparts as estimated by the brain shift correction framework. When considering moderate and high shift ([Formula: see text], [Formula: see text] measurements per case), the alignment error due to brain shift reduced from [Formula: see text] to [Formula: see text], representing [Formula: see text] correction. These first steps toward validation are promising for model-based strategies.
Liao R, Ning L, Chen Z, Rigolo L, Gong S, Pasternak O, Golby AJ, Rathi Y, O'Donnell LJ, ckovic JV. Performance of Unscented Kalman Filter Tractography in Edema: Analysis of the Two-tensor Model. Neuroimage Clin. 2017;15 :819-31.Abstract
Diffusion MRI tractography is increasingly used in pre-operative neurosurgical planning to visualize critical fiber tracts. However, a major challenge for conventional tractography, especially in patients with brain tumors, is tracing fiber tracts that are affected by vasogenic edema, which increases water content in the tissue and lowers diffusion anisotropy. One strategy for improving fiber tracking is to use a tractography method that is more sensitive than the traditional single-tensor streamline tractography. We performed experiments to assess the performance of two-tensor unscented Kalman filter (UKF) tractography in edema. UKF tractography fits a diffusion model to the data during fiber tracking, taking advantage of prior information from the previous step along the fiber. We studied UKF performance in a synthetic diffusion MRI digital phantom with simulated edema and in retrospective data from two neurosurgical patients with edema affecting the arcuate fasciculus and corticospinal tracts. We compared the performance of several tractography methods including traditional streamline, UKF single-tensor, and UKF two-tensor. To provide practical guidance on how the UKF method could be employed, we evaluated the impact of using various seed regions both inside and outside the edematous regions, as well as the impact of parameter settings on the tractography sensitivity. We quantified the sensitivity of different methods by measuring the percentage of the patient-specific fMRI activation that was reached by the tractography. We expected that diffusion anisotropy threshold parameters, as well as the inclusion of a free water model, would significantly influence the reconstruction of edematous WM fiber tracts, because edema increases water content in the tissue and lowers anisotropy. Contrary to our initial expectations, varying the fractional anisotropy threshold and including a free water model did not affect the UKF two-tensor tractography output appreciably in these two patient datasets. The most effective parameter for increasing tracking sensitivity was the generalized anisotropy (GA) threshold, which increased the length of tracked fibers when reduced to 0.075. In addition, the most effective seeding strategy was seeding in the whole brain or in a large region outside of the edema. Overall, the main contribution of this study is to provide insight into how UKF tractography can work, using a two-tensor model, to begin to address the challenge of fiber tract reconstruction in edematous regions near brain tumors.
Essayed WI, Zhang F, Unadkat P, Cosgrove RG, Golby AJ, O'Donnell LJ. White Matter Tractography for Neurosurgical Planning: A Topography-based Review of the Current State of the Art. Neuroimage Clin. 2017;15 :659-72.Abstract
We perform a review of the literature in the field of white matter tractography for neurosurgical planning, focusing on those works where tractography was correlated with clinical information such as patient outcome, clinical functional testing, or electro-cortical stimulation. We organize the review by anatomical location in the brain and by surgical procedure, including both supratentorial and infratentorial pathologies, and excluding spinal cord applications. Where possible, we discuss implications of tractography for clinical care, as well as clinically relevant technical considerations regarding the tractography methods. We find that tractography is a valuable tool in variable situations in modern neurosurgery. Our survey of recent reports demonstrates multiple potentially successful applications of white matter tractography in neurosurgery, with progress towards overcoming clinical challenges of standardization and interpretation.
O'Donnell LJ, Suter Y, Rigolo L, Kahali P, Zhang F, Norton I, Albi A, Olubiyi O, Meola A, Essayed WI, et al. Automated White Matter Fiber Tract Identification in Patients with Brain Tumors. Neuroimage Clin. 2017;13 :138-53.Abstract

We propose a method for the automated identification of key white matter fiber tracts for neurosurgical planning, and we apply the method in a retrospective study of 18 consecutive neurosurgical patients with brain tumors. Our method is designed to be relatively robust to challenges in neurosurgical tractography, which include peritumoral edema, displacement, and mass effect caused by mass lesions. The proposed method has two parts. First, we learn a data-driven white matter parcellation or fiber cluster atlas using groupwise registration and spectral clustering of multi-fiber tractography from healthy controls. Key fiber tract clusters are identified in the atlas. Next, patient-specific fiber tracts are automatically identified using tractography-based registration to the atlas and spectral embedding of patient tractography. Results indicate good generalization of the data-driven atlas to patients: 80% of the 800 fiber clusters were identified in all 18 patients, and 94% of the 800 fiber clusters were found in 16 or more of the 18 patients. Automated subject-specific tract identification was evaluated by quantitative comparison to subject-specific motor and language functional MRI, focusing on the arcuate fasciculus (language) and corticospinal tracts (motor), which were identified in all patients. Results indicate good colocalization: 89 of 95, or 94%, of patient-specific language and motor activations were intersected by the corresponding identified tract. All patient-specific activations were within 3mm of the corresponding language or motor tract. Overall, our results indicate the potential of an automated method for identifying fiber tracts of interest for neurosurgical planning, even in patients with mass lesions.