Publications by Year: 2022


Yue Yu, George Bourantas, Benjamin Zwick, Grand Joldes, Tina Kapur, Sarah Frisken, Ron Kikinis, Arya Nabavi, Alexandra Golby, Adam Wittek, and Karol Miller. 2022. Computer Simulation of Tumour Resection-Induced Brain Deformation by a Meshless Approach. Int J Numer Method Biomed Eng, 38, 1, Pp. e3539.
Tumour resection requires precise planning and navigation to maximise tumour removal while simultaneously protecting nearby healthy tissues. Neurosurgeons need to know the location of the remaining tumour after partial tumour removal before continuing with the resection. Our approach to the problem uses biomechanical modelling and computer simulation to compute the brain deformations after the tumour is resected. In this study, we use meshless Total Lagrangian explicit dynamics as the solver. The problem geometry is extracted from the patient-specific magnetic resonance imaging (MRI) data and includes the parenchyma, tumour, cerebrospinal fluid and skull. The appropriate non-linear material formulation is used. Loading is performed by imposing intra-operative conditions of gravity and reaction forces between the tumour and surrounding healthy parenchyma tissues. A finite frictionless sliding contact is enforced between the skull (rigid) and parenchyma. The meshless simulation results are compared to intra-operative MRI sections. We also calculate Hausdorff distances between the computed deformed surfaces (ventricles and tumour cavities) and surfaces observed intra-operatively. Over 80% of points on the ventricle surface and 95% of points on the tumour cavity surface were successfully registered (results within the limits of two times the original in-plane resolution of the intra-operative image). Computed results demonstrate the potential for our method in estimating the tissue deformation and tumour boundary during the resection.
Lena Maier-Hein, Matthias Eisenmann, Duygu Sarikaya, Keno März, Toby Collins, Anand Malpani, Johannes Fallert, Hubertus Feussner, Stamatia Giannarou, Pietro Mascagni, Hirenkumar Nakawala, Adrian Park, Carla Pugh, Danail Stoyanov, Swaroop S Vedula, Kevin Cleary, Gabor Fichtinger, Germain Forestier, Bernard Gibaud, Teodor Grantcharov, Makoto Hashizume, Doreen Heckmann-Nötzel, Hannes G Kenngott, Ron Kikinis, Lars Mündermann, Nassir Navab, Sinan Onogur, Tobias Roß, Raphael Sznitman, Russell H Taylor, Minu D Tizabi, Martin Wagner, Gregory D Hager, Thomas Neumuth, Nicolas Padoy, Justin Collins, Ines Gockel, Jan Goedeke, Daniel A Hashimoto, Luc Joyeux, Kyle Lam, Daniel R Leff, Amin Madani, Hani J Marcus, Ozanan Meireles, Alexander Seitel, Dogu Teber, Frank Ückert, Beat P Müller-Stich, Pierre Jannin, and Stefanie Speidel. 2022. Surgical Data Science - From Concepts Toward Clinical Translation. Med Image Anal, 76, Pp. 102306.
Recent developments in data science in general and machine learning in particular have transformed the way experts envision the future of surgery. Surgical Data Science (SDS) is a new research field that aims to improve the quality of interventional healthcare through the capture, organization, analysis and modeling of data. While an increasing number of data-driven approaches and clinical applications have been studied in the fields of radiological and clinical data science, translational success stories are still lacking in surgery. In this publication, we shed light on the underlying reasons and provide a roadmap for future advances in the field. Based on an international workshop involving leading researchers in the field of SDS, we review current practice, key achievements and initiatives as well as available standards and tools for a number of topics relevant to the field, namely (1) infrastructure for data acquisition, storage and access in the presence of regulatory constraints, (2) data annotation and sharing and (3) data analytics. We further complement this technical perspective with (4) a review of currently available SDS products and the translational progress from academia and (5) a roadmap for faster clinical translation and exploitation of the full potential of SDS, based on an international multi-round Delphi process.
Thomas Guttuso, Daniel Sirica, Duygu Tosun, Robert Zivadinov, Ofer Pasternak, Daniel Weintraub, Francesca Baglio, and Niels Bergsland. 2022. Thalamic Dorsomedial Nucleus Free Water Correlates with Cognitive Decline in Parkinson’s Disease. Mov Disord, 37, 3, Pp. 490-501.
BACKGROUND: Brain diffusion tensor imaging (DTI) has been shown to reflect cognitive changes in early Parkinson s disease (PD) but the diffusion-based measure free water (FW) has not been previously assessed. OBJECTIVES: To assess if FW in the thalamic nuclei primarily involved with cognition (ie, the dorsomedial [DMN] and anterior [AN] nuclei), the nucleus basalis of Meynert (nbM), and the hippocampus correlates with and is associated with longitudinal cognitive decline and distinguishes cognitive status at baseline in early PD. Also, to explore how FW compares with conventional DTI, FW-corrected DTI, and volumetric assessments for these outcomes. METHODS: Imaging data and Montreal Cognitive Assessment (MoCA) scores from the Parkinson’s Progression Markers Initiative database were analyzed using partial correlations and ANCOVA. Primary outcome multiple comparisons were corrected for false discovery rate (q value). RESULTS: Thalamic DMN FW changes over 1 year correlated with MoCA changes over both 1 and 3 years (partial correlations -0.222, q = 0.040, n = 130; and - 0.229, q = 0.040, n = 123, respectively; mean PD duration at baseline = 6.85 months). NbM FW changes over 1 year only correlated with MoCA changes over 3 years (-0.222, q = 0.040). Baseline hippocampal FW was associated with cognitive impairment at 3 years (q = 0.040) and baseline nbM FW distinguished PD-normal cognition (MoCA >=26) from PD-cognitive impairment (MoCA
Sean D McGarry, Michael Brehler, John D Bukowy, Allison K Lowman, Samuel A Bobholz, Savannah R Duenweg, Anjishnu Banerjee, Sarah L Hurrell, Dariya Malyarenko, Thomas L Chenevert, Yue Cao, Yuan Li, Daekeun You, Andrey Fedorov, Laura C Bell, C, Melissa A Prah, Kathleen M Schmainda, Bachir Taouli, Eve LoCastro, Yousef Mazaheri, Amita Shukla-Dave, Thomas E Yankeelov, David A Hormuth, Ananth J Madhuranthakam, Keith Hulsey, Kurt Li, Wei Huang, Wei Huang, Mark Muzi, Michael A Jacobs, Meiyappan Solaiyappan, Stefanie Hectors, Tatjana Antic, Gladell P Paner, Watchareepohn Palangmonthip, Kenneth Jacobsohn, Mark Hohenwalter, Petar Duvnjak, Michael Griffin, William See, Marja T Nevalainen, Kenneth A Iczkowski, and Peter S LaViolette. 2022. Multi-Site Concordance of Diffusion-Weighted Imaging Quantification for Assessing Prostate Cancer Aggressiveness. J Magn Reson Imaging, 55, 6, Pp. 1745-58.
BACKGROUND: Diffusion-weighted imaging (DWI) is commonly used to detect prostate cancer, and a major clinical challenge is differentiating aggressive from indolent disease. PURPOSE: To compare 14 site-specific parametric fitting implementations applied to the same dataset of whole-mount pathologically validated DWI to test the hypothesis that cancer differentiation varies with different fitting algorithms. STUDY TYPE: Prospective. POPULATION: Thirty-three patients prospectively imaged prior to prostatectomy. FIELD STRENGTH/SEQUENCE: 3 T, field-of-view optimized and constrained undistorted single-shot DWI sequence. ASSESSMENT: Datasets, including a noise-free digital reference object (DRO), were distributed to the 14 teams, where locally implemented DWI parameter maps were calculated, including mono-exponential apparent diffusion coefficient (MEADC), kurtosis (K), diffusion kurtosis (DK), bi-exponential diffusion (BID), pseudo-diffusion (BID*), and perfusion fraction (F). The resulting parametric maps were centrally analyzed, where differentiation of benign from cancerous tissue was compared between DWI parameters and the fitting algorithms with a receiver operating characteristic area under the curve (ROC AUC). STATISTICAL TEST: Levene’s test, P < 0.05 corrected for multiple comparisons was considered statistically significant. RESULTS: The DRO results indicated minimal discordance between sites. Comparison across sites indicated that K, DK, and MEADC had significantly higher prostate cancer detection capability (AUC range = 0.72-0.76, 0.76-0.81, and 0.76-0.80 respectively) as compared to bi-exponential parameters (BID, BID*, F) which had lower AUC and greater between site variation (AUC range = 0.53-0.80, 0.51-0.81, and 0.52-0.80 respectively). Post-processing parameters also affected the resulting AUC, moving from, for example, 0.75 to 0.87 for MEADC varying cluster size. DATA CONCLUSION: We found that conventional diffusion models had consistent performance at differentiating prostate cancer from benign tissue. Our results also indicated that post-processing decisions on DWI data can affect sensitivity and specificity when applied to radiological-pathological studies in prostate cancer. LEVEL OF EVIDENCE: 1 TECHNICAL EFFICACY: Stage 3.
Nina Zaks, Tjasa Velikonja, Muhammad A Parvaz, Jamie Zinberg, Monica Done, Daniel H Mathalon, Jean Addington, Kristin Cadenhead, Tyrone Cannon, Barbara Cornblatt, Thomas McGlashan, Diana Perkins, William S Stone, Ming Tsuang, Elaine Walker, Scott W Woods, Matcheri S Keshavan, Daniel J Buysse, Eva Velthorst, and Carrie E Bearden. 2022. Sleep Disturbance in Individuals at Clinical High Risk for Psychosis. Schizophr Bull, 48, 1, Pp. 111-21.
INTRODUCTION: Disturbed sleep is a common feature of psychotic disorders that is also present in the clinical high risk (CHR) state. Evidence suggests a potential role of sleep disturbance in symptom progression, yet the interrelationship between sleep and CHR symptoms remains to be determined. To address this knowledge gap, we examined the association between disturbed sleep and CHR symptoms over time. METHODS: Data were obtained from the North American Prodrome Longitudinal Study (NAPLS)-3 consortium, including 688 CHR individuals and 94 controls (mean age 18.25, 46% female) for whom sleep was tracked prospectively for 8 months. We used Cox regression analyses to investigate whether sleep disturbances predicted conversion to psychosis up to >2 years later. With regressions and cross-lagged panel models, we analyzed longitudinal and bidirectional associations between sleep (the Pittsburgh Sleep Quality Index in conjunction with additional sleep items) and CHR symptoms. We also investigated the independent contribution of individual sleep characteristics on CHR symptom domains separately and explored whether cognitive impairments, stress, depression, and psychotropic medication affected the associations. RESULTS: Disturbed sleep at baseline did not predict conversion to psychosis. However, sleep disturbance was strongly correlated with heightened CHR symptoms over time. Depression accounted for half of the association between sleep and symptoms. Importantly, sleep was a significant predictor of CHR symptoms but not vice versa, although bidirectional effect sizes were similar. DISCUSSION: The critical role of sleep disturbance in CHR symptom changes suggests that sleep may be a promising intervention target to moderate outcome in the CHR state.
Amirhossein Bayat, Danielle F Pace, Anjany Sekuboyina, Christian Payer, Darko Stern, Martin Urschler, Jan S Kirschke, and Bjoern H Menze. 2022. Anatomy-Aware Inference of the 3D Standing Spine Posture from 2D Radiographs. Tomography, 8, 1, Pp. 479-96.
An important factor for the development of spinal degeneration, pain and the outcome of spinal surgery is known to be the balance of the spine. It must be analyzed in an upright, standing position to ensure physiological loading conditions and visualize load-dependent deformations. Despite the complex 3D shape of the spine, this analysis is currently performed using 2D radiographs, as all frequently used 3D imaging techniques require the patient to be scanned in a prone position. To overcome this limitation, we propose a deep neural network to reconstruct the 3D spinal pose in an upright standing position, loaded naturally. Specifically, we propose a novel neural network architecture, which takes orthogonal 2D radiographs and infers the spine’s 3D posture using vertebral shape priors. In this work, we define vertebral shape priors using an atlas and a spine shape prior, incorporating both into our proposed network architecture. We validate our architecture on digitally reconstructed radiographs, achieving a 3D reconstruction Dice of 0.95, indicating an almost perfect 2D-to-3D domain translation. Validating the reconstruction accuracy of a 3D standing spine on real data is infeasible due to the lack of a valid ground truth. Hence, we design a novel experiment for this purpose, using an orientation invariant distance metric, to evaluate our model’s ability to synthesize full-3D, upright, and patient-specific spine models. We compare the synthesized spine shapes from clinical upright standing radiographs to the same patient’s 3D spinal posture in the prone position from CT.
Junxiao Zheng, Qinzhu Yang, Nikos Makris, Kaibin Huang, Jianwen Liang, Chenfei Ye, Xiaxia Yu, Mu Tian, Ting Ma, Tian Mou, Wenlong Guo, Ron Kikinis, and Yi Gao. 2022. Three-Dimensional Digital Reconstruction of the Cerebellar Cortex: Lobule Thickness, Surface Area Measurements, and Layer Architecture. Cerebellum.
The cerebellum is ontogenetically one of the first structures to develop in the central nervous system; nevertheless, it has been only recently reconsidered for its significant neurobiological, functional, and clinical relevance in humans. Thus, it has been a relatively under-studied compared to the cerebrum. Currently, non-invasive imaging modalities can barely reach the necessary resolution to unfold its entire, convoluted surface, while only histological analyses can reveal local information at the micrometer scale. Herein, we used the BigBrain dataset to generate area and point-wise thickness measurements for all layers of the cerebellar cortex and for each lobule in particular. We found that the overall surface area of the cerebellar granular layer (including Purkinje cells) was 1,732 cm2 and the molecular layer was 1,945 cm2. The average thickness of the granular layer is 0.88 mm (± 0.83) and that of the molecular layer is 0.32 mm (± 0.08). The cerebellum (both granular and molecular layers) is thicker at the depth of the sulci and thinner at the crowns of the gyri. Globally, the granular layer is thicker in the lateral-posterior-inferior region than the medial-superior regions. The characterization of individual layers in the cerebellum achieved herein represents a stepping-stone for investigations interrelating structural and functional connectivity with cerebellar architectonics using neuroimaging, which is a matter of considerable relevance in basic and clinical neuroscience. Furthermore, these data provide templates for the construction of cerebellar topographic maps and the precise localization of structural and functional alterations in diseases affecting the cerebellum.
Shuyue Wang, Fan Zhang, Peiyu Huang, Hui Hong, Yeerfan Jiaerken, Xinfeng Yu, Ruiting Zhang, Qingze Zeng, Yao Zhang, Ron Kikinis, Yogesh Rathi, Nikos Makris, Min Lou, Ofer Pasternak, Minming Zhang, and Lauren J O Donnell. 2022. Superficial White Matter Microstructure Affects Processing Speed in Cerebral Small Vessel Disease. Hum Brain Mapp, 43, 17, Pp. 5310-25.
White matter hyperintensities (WMH) are a typical feature of cerebral small vessel disease (CSVD), which contributes to about 50% of dementias worldwide. Microstructural alterations in deep white matter (DWM) have been widely examined in CSVD. However, little is known about abnormalities in superficial white matter (SWM) and their relevance for processing speed, the main cognitive deficit in CSVD. In 141 CSVD patients, processing speed was assessed using Trail Making Test Part A. White matter abnormalities were assessed by WMH burden (volume on T2-FLAIR) and diffusion MRI measures. SWM imaging measures had a large contribution to processing speed, despite a relatively low SWM WMH burden. Across all imaging measures, SWM free water (FW) had the strongest association with processing speed, followed by SWM mean diffusivity (MD). SWM FW was the only marker to significantly increase between two subgroups with the lowest WMH burdens. When comparing two subgroups with the highest WMH burdens, the involvement of WMH in the SWM was accompanied by significant differences in processing speed and white matter microstructure. Mediation analysis revealed that SWM FW fully mediated the association between WMH volume and processing speed, while no mediation effect of MD or DWM FW was observed. Overall, results suggest that the SWM has an important contribution to processing speed, while SWM FW is a sensitive imaging marker associated with cognition in CSVD. This study extends the current understanding of CSVD-related dysfunction and suggests that the SWM, as an understudied region, can be a potential target for monitoring pathophysiological processes.
Sonia Pujol, Ryan P Cabeen, Jérôme Yelnik, Chantal François, Sara Fernandez Vidal, Carine Karachi, Eric Bardinet, G, and Ron Kikinis. 2022. Somatotopic Organization of Hyperdirect Pathway Projections From the Primary Motor Cortex in the Human Brain. Front Neurol, 13, Pp. 791092.
Background: The subthalamic nucleus (STN) is an effective neurosurgical target to improve motor symptoms in Parkinson s Disease (PD) patients. MR-guided Focused Ultrasound (MRgFUS) subthalamotomy is being explored as a therapeutic alternative to Deep Brain Stimulation (DBS) of the STN. The hyperdirect pathway provides a direct connection between the cortex and the STN and is likely to play a key role in the therapeutic effects of MRgFUS intervention in PD patients. Objective: This study aims to investigate the topography and somatotopy of hyperdirect pathway projections from the primary motor cortex (M1). Methods: We used advanced multi-fiber tractography and high-resolution diffusion MRI data acquired on five subjects of the Human Connectome Project (HCP) to reconstruct hyperdirect pathway projections from M1. Two neuroanatomy experts reviewed the anatomical accuracy of the tracts. We extracted the fascicles arising from the trunk, arm, hand, face and tongue area from the reconstructed pathways. We assessed the variability among subjects based on the fractional anisotropy (FA) and mean diffusivity (MD) of the fibers. We evaluated the spatial arrangement of the different fascicles using the Dice Similarity Coefficient (DSC) of spatial overlap and the centroids of the bundles. Results: We successfully reconstructed hyperdirect pathway projections from M1 in all five subjects. The tracts were in agreement with the expected anatomy. We identified hyperdirect pathway fascicles projecting from the trunk, arm, hand, face and tongue area in all subjects. Tract-derived measurements showed low variability among subjects, and similar distributions of FA and MD values among the fascicles projecting from different M1 areas. We found an anterolateral somatotopic arrangement of the fascicles in the corona radiata, and an average overlap of 0.63 in the internal capsule and 0.65 in the zona incerta. Conclusion: Multi-fiber tractography combined with high-resolution diffusion MRI data enables the identification of the somatotopic organization of the hyperdirect pathway. Our preliminary results suggest that the subdivisions of the hyperdirect pathway projecting from the trunk, arm, hand, face, and tongue motor area are intermixed at the level of the zona incerta and posterior limb of the internal capsule, with a predominantly overlapping topographical organization in both regions. Subject-specific knowledge of the hyperdirect pathway somatotopy could help optimize target definition in MRgFUS intervention.