Yukiko Saito, Marek Kubicki, Inga Koerte, Tatsui Otsuka, Yogesh Rathi, Ofer Pasternak, Sylvain Bouix, Ryan Eckbo, Zora Kikinis, Christian Clemm von Hohenberg, Tomohide Roppongi, Elisabetta Del Re, Takeshi Asami, Sang-Hyuk Lee, Sarina Karmacharya, Raquelle I Mesholam-Gately, Larry J Seidman, James Levitt, Robert W McCarley, Martha E Shenton, and Margaret A Niznikiewicz. 2/2018. “Impaired White Matter Connectivity between Regions Containing Mirror Neurons, and Relationship to Negative Symptoms and Social Cognition, in Patients with First-Episode Schizophrenia.” Brain Imaging Behav, 12, 1, Pp. 229-37.Abstract
In schizophrenia, abnormalities in structural connectivity between brain regions known to contain mirror neurons and their relationship to negative symptoms related to a domain of social cognition are not well understood. Diffusion tensor imaging (DTI) scans were acquired in 16 patients with first episode schizophrenia and 16 matched healthy controls. FA and Trace of the tracts interconnecting regions known to be rich in mirror neurons, i.e., anterior cingulate cortex (ACC), inferior parietal lobe (IPL) and premotor cortex (PMC) were evaluated. A significant group effect for Trace was observed in IPL-PMC white matter fiber tract (F (1, 28) = 7.13, p = .012), as well as in the PMC-ACC white matter fiber tract (F (1, 28) = 4.64, p = .040). There were no group differences in FA. In addition, patients with schizophrenia showed a significant positive correlation between the Trace of the left IPL-PMC white matter fiber tract, and the Ability to Feel Intimacy and Closeness score (rho = .57, p = 0.034), and a negative correlation between the Trace of the left PMC-ACC and the Relationships with Friends and Peers score (rho = remove -.54, p = 0.049). We have demonstrated disrupted white mater microstructure within the white matter tracts subserving brain regions containing mirror neurons. We further showed that such structural disruptions might impact negative symptoms and, more specifically, contribute to the inability to feel intimacy (a measure conceptually related to theory of mind) in first episode schizophrenia. Further studies are needed to understand the potential of our results for diagnosis, prognosis and therapeutic interventions.
David Black, Michael Unger, Nele Fischer, Ron Kikinis, Horst Hahn, Thomas Neumuth, and Bernhard Glaser. 1/2018. “Auditory Display as Feedback for a Novel Eye-tracking System for Sterile Operating Room Interaction.” Int J Comput Assist Radiol Surg, 13, 1, Pp. 37-45.Abstract
PURPOSE: The growing number of technical systems in the operating room has increased attention on developing touchless interaction methods for sterile conditions. However, touchless interaction paradigms lack the tactile feedback found in common input devices such as mice and keyboards. We propose a novel touchless eye-tracking interaction system with auditory display as a feedback method for completing typical operating room tasks. Auditory display provides feedback concerning the selected input into the eye-tracking system as well as a confirmation of the system response. METHODS: An eye-tracking system with a novel auditory display using both earcons and parameter-mapping sonification was developed to allow touchless interaction for six typical scrub nurse tasks. An evaluation with novice participants compared auditory display with visual display with respect to reaction time and a series of subjective measures. RESULTS: When using auditory display to substitute for the lost tactile feedback during eye-tracking interaction, participants exhibit reduced reaction time compared to using visual-only display. In addition, the auditory feedback led to lower subjective workload and higher usefulness and system acceptance ratings. CONCLUSION: Due to the absence of tactile feedback for eye-tracking and other touchless interaction methods, auditory display is shown to be a useful and necessary addition to new interaction concepts for the sterile operating room, reducing reaction times while improving subjective measures, including usefulness, user satisfaction, and cognitive workload.
David Black, Horst K Hahn, Ron Kikinis, Karin Wårdell, and Neda Haj-Hosseini. 1/2018. “Auditory Display for Fluorescence-guided Open Brain Tumor Surgery.” Int J Comput Assist Radiol Surg, 13, 1, Pp. 25-35.Abstract
PURPOSE: Protoporphyrin (PpIX) fluorescence allows discrimination of tumor and normal brain tissue during neurosurgery. A handheld fluorescence (HHF) probe can be used for spectroscopic measurement of 5-ALA-induced PpIX to enable objective detection compared to visual evaluation of fluorescence. However, current technology requires that the surgeon either views the measured values on a screen or employs an assistant to verbally relay the values. An auditory feedback system was developed and evaluated for communicating measured fluorescence intensity values directly to the surgeon. METHODS: The auditory display was programmed to map the values measured by the HHF probe to the playback of tones that represented three fluorescence intensity ranges and one error signal. Ten persons with no previous knowledge of the application took part in a laboratory evaluation. After a brief training period, participants performed measurements on a tray of 96 wells of liquid fluorescence phantom and verbally stated the perceived measurement values for each well. The latency and accuracy of the participants' verbal responses were recorded. The long-term memorization of sound function was evaluated in a second set of 10 participants 2-3 and 7-12 days after training. RESULTS: The participants identified the played tone accurately for 98% of measurements after training. The median response time to verbally identify the played tones was 2 pulses. No correlation was found between the latency and accuracy of the responses, and no significant correlation with the musical proficiency of the participants was observed on the function responses. Responses for the memory test were 100% accurate. CONCLUSION: The employed auditory display was shown to be intuitive, easy to learn and remember, fast to recognize, and accurate in providing users with measurements of fluorescence intensity or error signal. The results of this work establish a basis for implementing and further evaluating auditory displays in clinical scenarios involving fluorescence guidance and other areas for which categorized auditory display could be useful.
Evren Özarslan, Cem Yolcu, Magnus Herberthson, Hans Knutsson, and Carl-Fredrik Westin. 1/2018. “Influence of the Size and Curvedness of Neural Projections on the Orientationally Averaged Diffusion MR Signal .” Front Phys, 6.Abstract
Neuronal and glial projections can be envisioned to be tubes of infinitesimal diameter as far as diffusion magnetic resonance (MR) measurements via clinical scanners are concerned. Recent experimental studies indicate that the decay of the orientationally-averaged signal in white-matter may be characterized by the power-law, () ∝ , where is the wavenumber determined by the parameters of the pulsed field gradient measurements. One particular study by McKinnon . [1] reports a distinctively faster decay in gray-matter. Here, we assess the role of the size and curvature of the neurites and glial arborizations in these experimental findings. To this end, we studied the signal decay for diffusion along general curves at all three temporal regimes of the traditional pulsed field gradient measurements. We show that for curvy projections, employment of longer pulse durations leads to a disappearance of the decay, while such decay is robust when narrow gradient pulses are used. Thus, in clinical acquisitions, the lack of such a decay for a fibrous specimen can be seen as indicative of fibers that are curved. We note that the above discussion is valid for an intermediate range of -values as the true asymptotic behavior of the signal decay is () ∝ for narrow pulses (through Debye-Porod law) or steeper for longer pulses. This study is expected to provide insights for interpreting the diffusion-weighted images of the central nervous system and aid in the design of acquisition strategies.
Matthew Toews and William M Wells. 1/2018. “Phantomless Auto-Calibration and Online Calibration Assessment for a Tracked Freehand 2-D Ultrasound Probe.” IEEE Trans Med Imaging, 37, 1, Pp. 262-72.Abstract
This paper presents a method for automatically calibrating and assessing the calibration quality of an externally tracked 2-D ultrasound (US) probe by scanning arbitrary, natural tissues, as opposed a specialized calibration phantom as is the typical practice. A generative topic model quantifies the posterior probability of calibration parameters conditioned on local 2-D image features arising from a generic underlying substrate. Auto-calibration is achieved by identifying the maximum a-posteriori image-to-probe transform, and calibration quality is assessed online in terms of the posterior probability of the current image-to-probe transform. Both are closely linked to the 3-D point reconstruction error (PRE) in aligning feature observations arising from the same underlying physical structure in different US images. The method is of practical importance in that it operates simply by scanning arbitrary textured echogenic structures, e.g., in-vivo tissues in the context of the US-guided procedures, without requiring specialized calibration procedures or equipment. Observed data take the form of local scale-invariant features that can be extracted and fit to the model in near real-time. Experiments demonstrate the method on a public data set of in vivo human brain scans of 14 unique subjects acquired in the context of neurosurgery. Online calibration assessment can be performed at approximately 3 Hz for the US images of pixels. Auto-calibration achieves an internal mean PRE of 1.2 mm and a discrepancy of [2 mm, 6 mm] in comparison to the calibration via a standard phantom-based method.
Adrian V Dalca, Katherine L Bouman, William T Freeman, Natalia S Rost, Mert R Sabuncu, and Polina Golland. 2018. “Medical Image Imputation from Image Collections.” IEEE Trans Med Imaging.Abstract
We present an algorithm for creating high resolution anatomically plausible images consistent with acquired clinical brain MRI scans with large inter-slice spacing. Although large data sets of clinical images contain a wealth of information, time constraints during acquisition result in sparse scans that fail to capture much of the anatomy. These characteristics often render computational analysis impractical as many image analysis algorithms tend to fail when applied to such images. Highly specialized algorithms that explicitly handle sparse slice spacing do not generalize well across problem domains. In contrast, we aim to enable application of existing algorithms that were originally developed for high resolution research scans to significantly undersampled scans. We introduce a generative model that captures fine-scale anatomical structure across subjects in clinical image collections and derive an algorithm for filling in the missing data in scans with large inter-slice spacing. Our experimental results demonstrate that the resulting method outperforms state-of-the-art upsampling super-resolution techniques, and promises to facilitate subsequent analysis not previously possible with scans of this quality. Our implementation is freely available at
Vivian Schultz, Robert A Stern, Yorghos Tripodis, Julie Stamm, Pawel Wrobel, Christian Lepage, Isabelle Weir, Jeffrey P Guenette, Alicia Chua, Michael L Alosco, Christine M Baugh, Nathan G Fritts, Brett M Martin, Christine E Chaisson, Michael J Coleman, Alexander P Lin, Ofer Pasternak, Martha E Shenton, and Inga K Koerte. 2018. “Age at First Exposure to Repetitive Head Impacts Is Associated with Smaller Thalamic Volumes in Former Professional American Football Players.” J Neurotrauma, 35, 2, Pp. 278-85.Abstract
Thalamic atrophy has been associated with exposure to repetitive head impacts (RHI) in professional fighters. The aim of this study is to investigate whether or not age at first exposure (AFE) to RHI is associated with thalamic volume in symptomatic former National Football League (NFL) players at risk for chronic traumatic encephalopathy (CTE). Eighty-six symptomatic former NFL players (mean age = 54.9 ± 7.9 years) were included. T1-weighted data were acquired on a 3T magnetic resonance imager, and thalamic volumes were derived using FreeSurfer. Mood and behavior, psychomotor speed, and visual and verbal memory were assessed. The association between thalamic volume and AFE to playing football and to number of years playing was calculated. Decreased thalamic volume was associated with more years of play (left: p = 0.03; right: p = 0.03). Younger AFE was associated with decreased right thalamic volume (p = 0.014). This association remained significant after adjusting for total years of play. Decreased left thalamic volume was associated with worse visual memory (p = 0.014), whereas increased right thalamic volume was associated with fewer mood and behavior symptoms (p = 0.003). In our sample of symptomatic former NFL players at risk for CTE, total years of play and AFE were associated with decreased thalamic volume. The effect of AFE on right thalamic volume was almost twice as strong as the effect of total years of play. Our findings confirm previous reports of an association between thalamic volume and exposure to RHI. They suggest further that younger AFE may result in smaller thalamic volume later in life.
Anna Custo, Dimitri Van De Ville, William M Wells, Miralena I Tomescu, Denis Brunet, and Christoph M Michel. 12/2017. “Electroencephalographic Resting-State Networks: Source Localization of Microstates.” Brain Connect, 7, 10, Pp. 671-82.Abstract
Using electroencephalography (EEG) to elucidate the spontaneous activation of brain resting-state networks (RSNs) is nontrivial as the signal of interest is of low amplitude and it is difficult to distinguish the underlying neural sources. Using the principles of electric field topographical analysis, it is possible to estimate the meta-stable states of the brain (i.e., the resting-state topographies, so-called microstates). We estimated seven resting-state topographies explaining the EEG data set with k-means clustering (N = 164, 256 electrodes). Using a method specifically designed to localize the sources of broadband EEG scalp topographies by matching sensor and source space temporal patterns, we demonstrated that we can estimate the EEG RSNs reliably by measuring the reproducibility of our findings. After subtracting their mean from the seven EEG RSNs, we identified seven state-specific networks. The mean map includes regions known to be densely anatomically and functionally connected (superior frontal, superior parietal, insula, and anterior cingulate cortices). While the mean map can be interpreted as a "router," crosslinking multiple functional networks, the seven state-specific RSNs partly resemble and extend previous functional magnetic resonance imaging-based networks estimated as the hemodynamic correlates of four canonical EEG microstates.
Klaus H Maier-Hein, Peter F Neher, Jean-Christophe Houde, Marc-Alexandre Côté, Eleftherios Garyfallidis, Jidan Zhong, Maxime Chamberland, Fang-Cheng Yeh, Ying-Chia Lin, Qing Ji, Wilburn E Reddick, John O Glass, David Qixiang Chen, Yuanjing Feng, Chengfeng Gao, Ye Wu, Jieyan Ma, H Renjie, Qiang Li, Carl-Fredrik Westin, Samuel Deslauriers-Gauthier, Omar Ocegueda J González, Michael Paquette, Samuel St-Jean, Gabriel Girard, François Rheault, Jasmeen Sidhu, Chantal MW Tax, Fenghua Guo, Hamed Y Mesri, Szabolcs Dávid, Martijn Froeling, Anneriet M Heemskerk, Alexander Leemans, Arnaud Boré, Basile Pinsard, Christophe Bedetti, Matthieu Desrosiers, Simona Brambati, Julien Doyon, Alessia Sarica, Roberta Vasta, Antonio Cerasa, Aldo Quattrone, Jason Yeatman, Ali R Khan, Wes Hodges, Simon Alexander, David Romascano, Muhamed Barakovic, Anna Auría, Oscar Esteban, Alia Lemkaddem, Jean-Philippe Thiran, Ertan H Cetingul, Benjamin L Odry, Boris Mailhe, Mariappan S Nadar, Fabrizio Pizzagalli, Gautam Prasad, Julio E Villalon-Reina, Justin Galvis, Paul M Thompson, Francisco De Santiago Requejo, Pedro Luque Laguna, Luis Miguel Lacerda, Rachel Barrett, Flavio Dell'Acqua, Marco Catani, Laurent Petit, Emmanuel Caruyer, Alessandro Daducci, Tim B Dyrby, Tim Holland-Letz, Claus C Hilgetag, Bram Stieltjes, and Maxime Descoteaux. 11/2017. “The Challenge of Mapping the Human Connectome Based on Diffusion Tractography.” Nat Commun, 8, 1, Pp. 1349.Abstract
Tractography based on non-invasive diffusion imaging is central to the study of human brain connectivity. To date, the approach has not been systematically validated in ground truth studies. Based on a simulated human brain data set with ground truth tracts, we organized an open international tractography challenge, which resulted in 96 distinct submissions from 20 research groups. Here, we report the encouraging finding that most state-of-the-art algorithms produce tractograms containing 90% of the ground truth bundles (to at least some extent). However, the same tractograms contain many more invalid than valid bundles, and half of these invalid bundles occur systematically across research groups. Taken together, our results demonstrate and confirm fundamental ambiguities inherent in tract reconstruction based on orientation information alone, which need to be considered when interpreting tractography and connectivity results. Our approach provides a novel framework for estimating reliability of tractography and encourages innovation to address its current limitations.
Lena KL Oestreich, Amanda E Lyall, Ofer Pasternak, Zora Kikinis, Dominick T Newell, Peter Savadjiev, Sylvain Bouix, Martha E Shenton, Marek Kubicki, Marek Kubicki, Thomas J Whitford, and Simon McCarthy-Jones. 11/2017. “Characterizing White Matter Changes in Chronic Schizophrenia: A Free-water Imaging Multi-site Study.” Schizophr Res, 189, Pp. 153-61.Abstract
Diffusion tensor imaging (DTI) studies in chronic schizophrenia have found widespread but often inconsistent patterns of white matter abnormalities. These studies have typically used the conventional measure of fractional anisotropy, which can be contaminated by extracellular free-water. A recent free-water imaging study reported reduced free-water corrected fractional anisotropy (FAT) in chronic schizophrenia across several brain regions, but limited changes in the extracellular volume. The present study set out to validate these findings in a substantially larger sample. Tract-based spatial statistics (TBSS) was performed in 188 healthy controls and 281 chronic schizophrenia patients. Forty-two regions of interest (ROIs), as well as average whole-brain FAT and FW were extracted from free-water corrected diffusion tensor maps. Compared to healthy controls, reduced FAT was found in the chronic schizophrenia group in the anterior limb of the internal capsule bilaterally, the posterior thalamic radiation bilaterally, as well as the genu and body of the corpus callosum. While a significant main effect of group was observed for FW, none of the follow-up contrasts survived correction for multiple comparisons. The observed FAT reductions in the absence of extracellular FW changes, in a large, multi-site sample of chronic schizophrenia patients, validate the pattern of findings reported by a previous, smaller free-water imaging study of a similar sample. The limited number of regions in which FAT was reduced in the schizophrenia group suggests that actual white matter tissue degeneration in chronic schizophrenia, independent of extracellular FW, might be more localized than suggested previously.
Joost JM van Griethuysen, Andriy Fedorov, Chintan Parmar, Ahmed Hosny, Nicole Aucoin, Vivek Narayan, Regina GH Beets-Tan, Jean-Christophe Fillion-Robin, Steve Pieper, and Hugo JWL Aerts. 11/2017. “Computational Radiomics System to Decode the Radiographic Phenotype.” Cancer Res, 77, 21, Pp. e104-e107.Abstract
Radiomics aims to quantify phenotypic characteristics on medical imaging through the use of automated algorithms. Radiomic artificial intelligence (AI) technology, either based on engineered hard-coded algorithms or deep learning methods, can be used to develop noninvasive imaging-based biomarkers. However, lack of standardized algorithm definitions and image processing severely hampers reproducibility and comparability of results. To address this issue, we developed , a flexible open-source platform capable of extracting a large panel of engineered features from medical images. is implemented in Python and can be used standalone or using 3D Slicer. Here, we discuss the workflow and architecture of and demonstrate its application in characterizing lung lesions. Source code, documentation, and examples are publicly available at With this platform, we aim to establish a reference standard for radiomic analyses, provide a tested and maintained resource, and to grow the community of radiomic developers addressing critical needs in cancer research. .
Christian Herz, Jean-Christophe Fillion-Robin, Michael Onken, Jörg Riesmeier, Andras Lasso, Csaba Pinter, Gabor Fichtinger, Steve Pieper, David Clunie, Ron Kikinis, and Andriy Fedorov. 11/2017. “DCMQI: An Open Source Library for Standardized Communication of Quantitative Image Analysis Results using DICOM.” Cancer Research, 77, 21, Pp. e87-e90.Abstract
Quantitative analysis of clinical image data is an active area of research that holds promise for precision medicine, early assessment of treatment response, and objective characterization of the disease. Interoperability, data sharing, and the ability to mine the resulting data are of increasing importance, given the explosive growth in the number of quantitative analysis methods being proposed. The Digital Imaging and Communications in Medicine (DICOM) standard is widely adopted for image and metadata in radiology. dcmqi (DICOM for Quantitative Imaging) is a free, open source library that implements conversion of the data stored in commonly used research formats into the standard DICOM representation. dcmqi source code is distributed under BSD-style license. It is freely available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer. Installation and usage instructions are provided on Harvard DASH.
Sarah Parisot, Ben Glocker, Sofia Ira Ktena, Salim Arslan, Markus D Schirmer, and Daniel Rueckert. 11/2017. “A Flexible Graphical Model for Multi-modal Parcellation of the Cortex .” Neuroimage, 162, Pp. 226-48.Abstract
Advances in neuroimaging have provided a tremendous amount of in-vivo information on the brain's organisation. Its anatomy and cortical organisation can be investigated from the point of view of several imaging modalities, many of which have been studied for mapping functionally specialised cortical areas. There is strong evidence that a single modality is not sufficient to fully identify the brain's cortical organisation. Combining multiple modalities in the same parcellation task has the potential to provide more accurate and robust subdivisions of the cortex. Nonetheless, existing brain parcellation methods are typically developed and tested on single modalities using a specific type of information. In this paper, we propose Graph-based Multi-modal Parcellation (GraMPa), an iterative framework designed to handle the large variety of available input modalities to tackle the multi-modal parcellation task. At each iteration, we compute a set of parcellations from different modalities and fuse them based on their local reliabilities. The fused parcellation is used to initialise the next iteration, forcing the parcellations to converge towards a set of mutually informed modality specific parcellations, where correspondences are established. We explore two different multi-modal configurations for group-wise parcellation using resting-state fMRI, diffusion MRI tractography, myelin maps and task fMRI. Quantitative and qualitative results on the Human Connectome Project database show that integrating multi-modal information yields a stronger agreement with well established atlases and more robust connectivity networks that provide a better representation of the population.
Isaiah Norton, Walid Ibn Essayed, Fan Zhang, Sonia Pujol, Alex Yarmarkovich, Alexandra J Golby, Gordon Kindlmann, Demian Wasserman, Raul San Jose Estepar, Yogesh Rathi, Steve Pieper, Ron Kikinis, Hans J Johnson, Carl-Fredrik Westin, and Lauren J O'Donnell. 11/2017. “SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research.” Cancer Res, 77, 21, Pp. 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.
Edward Ofori, Florian Krismer, Roxana G Burciu, Ofer Pasternak, Johanna L McCracken, Mechelle M Lewis, Guangwei Du, Nikolaus R McFarland, Michael S Okun, Werner Poewe, Christoph Mueller, Elke R Gizewski, Michael Schocke, Christian Kremser, Hong Li, Xuemei Huang, Klaus Seppi, and David E Vaillancourt. 10/2017. “Free Water Improves Detection of Changes in the Substantia Nigra in Parkinsonism: A Multisite Study.” Mov Disord, 32, 10, Pp. 1457-64.Abstract
BACKGROUND: Imaging markers that are sensitive to parkinsonism across multiple sites are critically needed for clinical trials. The objective of this study was to evaluate changes in the substantia nigra using single- and bi-tensor models of diffusion magnetic resonance imaging in PD, MSA, and PSP. METHODS: The study cohort (n = 425) included 107 healthy controls and 184 PD, 63 MSA, and 71 PSP patients from 3 movement disorder centers. Bi-tensor free water, free-water-corrected fractional anisotropy, free-water-corrected mean diffusivity, single-tensor fractional anisotropy, and single-tensor mean diffusivity were computed for the anterior and posterior substantia nigra. Correlations were computed between diffusion MRI measures and clinical measures. RESULTS: In the posterior substantia nigra, free water was greater for PSP than MSA and PD patients and controls. PD and MSA both had greater free water than controls. Free-water-corrected fractional anisotropy values were greater for PSP patents than for controls and PD patients. PSP and MSA patient single-tensor mean diffusivity values were greater than controls, and single-tensor fractional anisotropy values were lower for PSP patients than for healthy controls. The parkinsonism effect size for free water was 0.145 in the posterior substantia nigra and 0.072 for single-tensor mean diffusivity. The direction of correlations between single-tensor mean diffusivity and free-water values and clinical scores was similar at each site. CONCLUSIONS: Free-water values in the posterior substantia nigra provide a consistent pattern of findings across patients with PD, MSA, and PSP in a large cohort across 3 sites. Free water in the posterior substantia nigra relates to clinical measures of motor and cognitive symptoms in a large cohort of parkinsonism. © 2017 International Parkinson and Movement Disorder Society.
Miaomiao Zhang, William M Wells, and Polina Golland. 10/2017. “Probabilistic Modeling of Anatomical Variability using a Low Dimensional Parameterization of Diffeomorphisms.” Med Image Anal, 41, Pp. 55-62.Abstract
We present an efficient probabilistic model of anatomical variability in a linear space of initial velocities of diffeomorphic transformations and demonstrate its benefits in clinical studies of brain anatomy. To overcome the computational challenges of the high dimensional deformation-based descriptors, we develop a latent variable model for principal geodesic analysis (PGA) based on a low dimensional shape descriptor that effectively captures the intrinsic variability in a population. We define a novel shape prior that explicitly represents principal modes as a multivariate complex Gaussian distribution on the initial velocities in a bandlimited space. We demonstrate the performance of our model on a set of 3D brain MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Our model yields a more compact representation of group variation at substantially lower computational cost than the state-of-the-art method such as tangent space PCA (TPCA) and probabilistic principal geodesic analysis (PPGA) that operate in the high dimensional image space.
David Black, Christian Hansen, Arya Nabavi, Ron Kikinis, and Horst Hahn. 10/2017. “A Survey of Auditory Display in Image-guided Interventions.” Int J Comput Assist Radiol Surg, 12, 10, Pp. 1665-76.Abstract
PURPOSE: This article investigates the current state of the art of the use of auditory display in image-guided medical interventions. Auditory display is a means of conveying information using sound, and we review the use of this approach to support navigated interventions. We discuss the benefits and drawbacks of published systems and outline directions for future investigation. METHODS: We undertook a review of scientific articles on the topic of auditory rendering in image-guided intervention. This includes methods for avoidance of risk structures and instrument placement and manipulation. The review did not include auditory display for status monitoring, for instance in anesthesia. RESULTS: We identified 15 publications in the course of the search. Most of the literature (60%) investigates the use of auditory display to convey distance of a tracked instrument to an object using proximity or safety margins. The remainder discuss continuous guidance for navigated instrument placement. Four of the articles present clinical evaluations, 11 present laboratory evaluations, and 3 present informal evaluation (2 present both laboratory and clinical evaluations). CONCLUSION: Auditory display is a growing field that has been largely neglected in research in image-guided intervention. Despite benefits of auditory displays reported in both the reviewed literature and non-medical fields, adoption in medicine has been slow. Future challenges include increasing interdisciplinary cooperation with auditory display investigators to develop more meaningful auditory display designs and comprehensive evaluations which target the benefits and drawbacks of auditory display in image guidance.
Marc Niethammer, Kilian M Pohl, Firdaus Janoos, and William M Wells. 9/2017. “Active Mean Fields for Probabilistic Image Segmentation: Connections with Chan-Vese and Rudin-Osher-Fatemi Models.” SIAM J. Imaging Sci., 10, 3, Pp. 1069-1103.Abstract
Segmentation is a fundamental task for extracting semantically meaningful regions from an image. The goal of segmentation algorithms is to accurately assign object labels to each image location. However, image noise, shortcomings of algorithms, and image ambiguities cause uncertainty in label assignment. Estimating this uncertainty is important in multiple application domains, such as segmenting tumors from medical images for radiation treatment planning. One way to estimate these uncertainties is through the computation of posteriors of Bayesian models, which is computationally prohibitive for many practical applications. However, most computationally efficient methods fail to estimate label uncertainty. We therefore propose in this paper the active mean fields (AMF) approach, a technique based on Bayesian modeling that uses a mean-field approximation to efficiently compute a segmentation and its corresponding uncertainty. Based on a variational formulation, the resulting convex model combines any label-likelihood measure with a prior on the length of the segmentation boundary. A specific implementation of that model is the Chan-Vese segmentation model, in which the binary segmentation task is defined by a Gaussian likelihood and a prior regularizing the length of the segmentation boundary. Furthermore, the Euler-Lagrange equations derived from the AMF model are equivalent to those of the popular Rudin-Osher-Fatemi (ROF) model for image denoising. Solutions to the AMF model can thus be implemented by directly utilizing highly efficient ROF solvers on log-likelihood ratio fields. We qualitatively assess the approach on synthetic data as well as on real natural and medical images. For a quantitative evaluation, we apply our approach to the tt icgbench dataset.
David Black, Julian Hettig, Maria Luz, Christian Hansen, Ron Kikinis, and Horst Hahn. 9/2017. “Auditory Feedback to Support Image-Guided Medical Needle Placement.” Int J Comput Assist Radiol Surg, 12, 9, Pp. 1655-63.Abstract
PURPOSE: During medical needle placement using image-guided navigation systems, the clinician must concentrate on a screen. To reduce the clinician's visual reliance on the screen, this work proposes an auditory feedback method as a stand-alone method or to support visual feedback for placing the navigated medical instrument, in this case a needle. METHODS: An auditory synthesis model using pitch comparison and stereo panning parameter mapping was developed to augment or replace visual feedback for navigated needle placement. In contrast to existing approaches which augment but still require a visual display, this method allows view-free needle placement. An evaluation with 12 novice participants compared both auditory and combined audiovisual feedback against existing visual methods. RESULTS: Using combined audiovisual display, participants show similar task completion times and report similar subjective workload and accuracy while viewing the screen less compared to using the conventional visual method. The auditory feedback leads to higher task completion times and subjective workload compared to both combined and visual feedback. CONCLUSION: Audiovisual feedback shows promising results and establishes a basis for applying auditory feedback as a supplement to visual information to other navigated interventions, especially those for which viewing a patient is beneficial or necessary.
Ning Lipeng and Yogesh Rathi. 9/2017. “Dynamic Regression for Partial Correlation and Causality Analysis of Functional Brain Networks.” Int Conf Med Image Comput Comput Assist Interv. 20 (Pt1), Pp. 365-72.Abstract
We propose a general dynamic regression framework for partial correlation and causality analysis of functional brain networks. Using the optimal prediction theory, we present the solution of the dynamic regression problem by minimizing the entropy of the associated stochastic process. We also provide the relation between the solutions and the linear dependence models of Geweke and Granger and derive novel expressions for computing partial correlation and causality using an optimal prediction filter with minimum error variance. We use the proposed dynamic framework to study the intrinsic partial correlation and causal- ity between seven different brain networks using resting state functional MRI (rsfMRI) data from the Human Connectome Project (HCP) and compare our results with those obtained from standard correlation and causality measures. The results show that our optimal prediction filter explains a significant portion of the variance in the rsfMRI data at low frequencies, unlike standard partial correlation analysis.