Research

 

BCNI’s Basic and Clinical Research:  

The BCNI is continuously progressing along its mission and goals, to focus on collaborative efforts on multimodal brain imaging research and behavioral/clinical assessments. The BCNI has stressed and facilitated a more comprehensive strategy/approach beyond traditional analysis of dynamic brain imaging data, namely focusing on the state-of-the-art detailed underlying human brain network’s oscillations and functional connectivity/causality dynamics across 5 dimensions, and relating with sensory-motor, cognitive or behavioral correlates in the typical and atypical human brain.

The continuous mission is to better understand the basic biological and unified mechanisms of the underlying network function and task-specific functional and effective connectivity dynamics among local and large-scale networks, relevant for cognitive functions (attention, sensory integration, learning, memory and language), and for its alterations in cognitive disabilities and patients with neurological or psychiatric symptoms.

The continuing goal is to expand the integration of functional brain dynamics into multimodal structural and functional imaging, towards the quantification and development of neural markers for cognition, and neuro-diagnostic markers for disabilities and pathologies, allowing the better development and monitoring of interventional therapies.

Update of BCNI's overall Research Productivity (2017-2018):

The overall Research Output of the BCNI Institute during the past year (2017-2018) lists a total of 57 Publications (24 Papers and 33 Abstracts) of all researchers who are using the BCNI's platform and analysis pipelines, and the BCNI further provided a HQP training to about 20+ new scientists and students.

 

 
Specific Research Topics
  • Brain network oscillations, synchronization and connectivity in health and disease:

Based on successful pioneering and career-long team efforts, continuation of collaborative team-efforts with Lawrence Ward (UBC) and Sam Doesburg (SFU and former University Toronto) on better understanding the biology and neurophysiology of underlying brain network connectivity relating to sensori-motor and cognitive functions, and its alterations in cognitive disabilities and in patients with neurological or psychiatric symptoms. In particular the focus relates to brain network oscillation dynamics, its synchronization, cross-correlations across space/frequency/time, and task-specific functional connectivity dynamics among local and large-scale networks.

 

Synchronization and functional connectivity across the entire brain space in relation to clinical symptoms and consciousness: Conceptual Overview: We published conceptual overviews of current findings and their implications for how dynamic brain imaging technologies can be further used to probe structural, functional and temporal connectivity to better understand, diagnose and treat cognitive disabilities and neuro-psychiatric pathologies including the many forms of  traumatic brain injury.

  - Ribary, Doesburg and Ward. In Magnetoencephalography, 429-450, 2014.

  - Ribary and Ward, Phenomenological Neuropsychiatry, in press.

 

Proposed framework toward unified principles of cortical processing: Neural oscillations at various frequencies and their synchronization among brain areas have been associated with numerous cognitive processes, but strong theories to integrate such findings remain elusive. We introduced a neurophysiological mechanism or framework to explain how coordinated changes in neural oscillations across multiple frequency ranges could underlie functional brain activation and the formation of distributed functional ensembles across cortical and thalamocortical networks. These oscillatory network dynamics contribute to cognition across diverse contexts, as well as to its alteration in various neuro-psychiatric pathologies.

  - Ribary, Doesburg and Ward, Biomed. Eng. Lett., 2017.

  - Ribary, Doesburg and Ward, Magnetoencephalography, in press.

                                               

Brain network dynamics and connectivity underlying cognition (word reading) in collaboration with Lawrence Ward (UBC): We reported for the first time the fast dynamics of functional and effective (causal) brain network connectivity during word reading. These results, using high-density EEG imaging, highlight the interplay between local and long-distance neural dynamics involved at each stage of the reading process. In addition, in collaboration with Linda Siegel (UBC)  and Janet Chow (Burnaby School District) we further presented alterations in local and large-scale connectivity in children with Dyslexia pre/post interventional training programs.

  - Bedo, Ribary and Ward, PlusOne, 2014.

  - Bedo, Ender-Fox, Chow, Siegel, Ribary, and Ward. OHBM, 2018.

 

  • Alterations in brain network connectivity dynamics in children born very preterm:

In collaboration with PI Ruth Grunau (Pediatrics, UBC), Sam Doesburg (SFU), Teresa Cheung (SFU) and Anthony Herdman (UBC), we have stressed and facilitated a more comprehensive strategy/approach beyond tradional ones, namely focusing on the detailed underlying brain network’s oscillation and connectivity dynamics across 5 dimensions, and relating with cognitive or behavioral correlates: Imaging studies have provided some of the very first insights into how altered MEG oscillatory brain activity in developing brain networks underpins problems in the psychological development of these vulnerable children. We demonstrated (i) first experimental evidence of altered spontaneous neuromagnetic activity (oscillatory slowing) in children born very preterm, (ii) evidence that this altered resting activity is related to cognitive performance problems in preterm children, (iii) sequential activation within a network of cortical regions during short-term memory processing in school age children, (iv) specific differences in regional activation in very preterm children during short-term memory retention, (v) reliable patterns of communication and connectivity dynamics between brain regions during short-term memory retention in children age 6–10 years, (vi) first MEG evidence for altered patterns of communication and connectivity dynamics between brain regions in very preterm children, and (vii) that these highly specific alterations of functional connectivity in very preterm children are predictive of selective problems in cognitive development in these vulnerable children.

  - Doesburg, Herdman, Ribary, Cheung, Moiseev, Weinberg, Liotti, Weeks, Grunau. Exp. Brain Res., 4, 719-727, 2010.

  - Doesburg, Ribary, Herdman, Moiseev, Cheung, Miller, Poskitt, Weinberg, Whitfield, Synnes and Grunau. Pediatr. Res., 70, 171-176, 2011.

  - Doesburg, Ribary, Herdman, Miller, Poskitt, Moiseev, Whitfield, Synnes and Grunau. Neuroimage, 54, 2330-2339, 2011.

  - Doesburg, Chau, Cheung, Moiseev, Ribary, Herdman, Miller, Cepeda, Synnes and Grunau. Pain, 152, 1946-1952, 2013.

  - Bichin, Chau, Doesburg, Herdman, Ribary, Grunau, NDN, 2016.

  - Kozhemiako, Nunes, Vakorin, Chau, Moiseev, Bichin, Ribary, Grunau, Doesburg. Biomag 2018.

 

In addition and more recently, further BCNI analysis provided the first source-based analysis of task-dependent neuromagnetic connectivity in children born very prematurely. Atypical oscillatory synchronization during short term memory processes suggested disruption of interregional functional connectivity supporting cognition.  We demonstrated altered coherence in multiple frequency ranges, but identified alpha, beta and low-gamma band frequency ranges as particular pertinent to reduced functional interactions among brain areas in this group.  We further identified specific brain regions as expressing reduced task-dependent functional connectivity and dynamics, including middle frontal gyrus, suggesting impaired ability to recruit sufficient coordinated activity among frontal and widespread cortical regions which may further contribute to a better understanding of difficulties in executive abilities in children born very preterm.

  - Moiseev, Doesburg, Herdman, Ribary, Grunau. Brain Topography, 2015.

 

  • Altered Brain network connectivity dynamics in individuals with Down Syndrome (DS)

In collaboration with PI Naz Virji-Babul (UBC), Teresa Cheung (SFU) and Doug Cheyne (University Toronto), we have stressed and facilitated a more comprehensive strategy/approach beyond tradional ones, namely focusing on the detailed underlying brain network’s oscillation and connectivity dynamics across 5 dimensions, and relating with cognitive or behavioral correlates:

 

Mirror Neuron System in Down syndrome (DS): Functional brain imaging data indicated a dysfunction in the execution/observation mirror neuron system in subjects with DS. Motor responses were strongly lateralized to the ipsilateral rather than the contralateral side during execution, and the underlying functional connectivity dynamics was altered during sensory-motor integration. These data shed more light on how subjects with DS may differently understand the actions and intentions of others.

  - Virji-Babul N, Moiseev A, Cheung T, Weeks D, Cheyne D, and Ribary U. Hum. Brain Mapp., 31,160-171, 2010.

  - Virji-Babul N, Moiseev A, Cheung T, Weeks D, Cheyne D, and Ribary U. Am. J. Intellect. Dev. Disabil., 115, 113-127, 2010.

 

Voluntary movement in Down syndrome (DS): In the DS population, we observed two distinct patterns of neural activation of motor networks, (i) an ipsilateral dominance and (ii) a typical contralateral dominance, both in conjunction with altered underlying functional network connectivity dynamics, indicating a possible neurophysiological explanation related to differences in sensorimotor organization in DS.

  - Virji-Babul N, Moiseev A, Moiseeva N, Sun W, Ribary U, and Lott I. NeuroReport, 22, 358-364, 2011.

 

Perception of human motion: Functional brain imaging data indicated that perception of both, random or human motion involves de-synchronization of oscillatory activity in alpha/beta bands in similar cortical regions. However, only human motion was associated with a larger network and further related significant alterations in the alpha/beta band particularly in the right hemisphere, in addition to persistent increases in the gamma band. These data suggest that the visual perception of dynamic motion relates to de~/synchronized oscillatory activity of neuronal populations in distinct frequency bands, with activation of occipital and parietal regions in the early stages of processing, and subsequently of task-specific cortical locations.

  - Virji-Babul N, Moiseev A, Sun W, Fesharaki A, Beg F, and Ribary U. NeuroReport, 23, 793–798, 2012.

 

  • Expansion of MEG technology strategies and new applications

In collaboration with Ash Parameswaran (Engineering, SFU) and Karen Kavanagh (Physics, SFU), Teresa Cheung (BCNI, SFU) explored and expanded MEG technology strategies for (1) assessing the accuracy and explanation of MEG brain imaging data, focusing on a scanner independent approach to modeling neural activity with a hardware phantom model, and (2) developing new MEG applications towards the assessment of biochemical compounds in the human brain/body, focusing on a new technique for magnetic nanoparticle imaging using magnetoencephalography frequency data.

  - Cheung, T, Wong, J, Parameswaran, A, Babul, A, Beg, F, Kavanagh, KL, Jirasek, A, and Ribary, U. In: Biomagnetism: Interdisciplinary Research and Exploration; R.Kakigi, et al. eds, Hokkaido University Press, pp: 89-91, 2008.

  - Cheung, T, Kavanagh, KL, Ribary, U. IFMBE Proceedings, 28, 443-446, 2010.

 

  • Advancing the analysis of multimodal brain imaging and correlation to behavioral and clinical observations.

Collaborations with Todd Woodward (Psychiatry, UBC) and colleagues and provision of funding support on behalf of the BCNI for expanding their existing constrained PCA analysis on fMRI data, to be combined (i) with MEG dynamic brain imaging data, and (ii) with EEG dynamic brain imaging data, to achieve a multimodal analysis matrix including structural/ functional imaging (MRI, fMRI, MEG, EEG) and clinical-behavioral observation parameters.

In particular, a continuing development of multivariate fMRI software and application of Constrained Principal Component Analysis (cPCA). The services provide a user-friendly functional GUI that affords (a) all matrix combinations available to cPCA ; (b) multi-platform compatibility (Linux, Windows, and Macintosh); (c) incorporation of HRF and FIR models from SPM, FSL or AFNI; (d) output functions that produce brain images and also graphs of predictor weights that estimate the hemodynamic response associated with each component, (e) significance tests on the components for effect of the conditions of interest for MRI/fMRI and MEG/EEG data.

Chau CMY, Doesburg SM, Ribary U, Ranger M, Miller SP, Synnes A, Woodward TS, Grunau RE. Pediatric Academic Societies, 2015.

- Whitman JC, Takane Y, Cheung TPL, Moiseev A, Ribary U, Ward LM, Woodward TS. NeuroImage, 2016.

 

  • Collaborative Team-effort with National Neuroethics Core (UBC)

Collaborative team-effort with Judy Illes (UBC), Adrian Owen (Western University) and colleagues on Neuroimaging for Disorders of Consciousness (DOC): Charting the Canadian Ethics Landscape. The goal is to establish ethics guidelines for implementing multimodal brain imaging findings on Disorders of Consciousness into clinical practice. In light of promising brain imaging research advances, it is important to identify and address ethical, legal, and policy challenges at the interface of translation to clinical care. To this end, we conducted semi-structured interviews with physicians, lawyers, ethicists, and researchers selected for their expertise with this subject. We probed their concerns about using signals of consciousness for communication, diagnosis or treatment of patients with impaired consciousness.

  - Lee G, Byram AC, Owen AM, Ribary U, Stoessl J, Townson A, Stables C, and Illes J. Canadian J. Neurol. Sciences, 2015.

  - Illes et al. Can J. Neurol. Sci., 2016.

  - Byram AC, Lee G, Owen AM, Ribary U, Stoessl J, Townson A, Illes J. CQHE, 2016.

 

  • Setup of a Research Consortium on Dyslexia

PI (BCNI Director) and collaborative expert teams across SFU, BCCH-Research Institute, UBC, Canada and the USA including the BC school system. The comprehensive research consortium includes behavioral assessments, multimodal brain imaging (MRI, fMRI, pEEG, MEG, pEye-Tracking)) applied pre- and post interventional training programs, and neuroethics in conjunction with children at BC schools towards a better understanding of the underlying integration problems and brain network connectivity in language disabilities and its possible plastic restorations. We are currently approaching the necessary larger funding sources.

 

Pilot Project - 2014-present: As PI and in collaboration with Linda Siegel (UBC), Lawrence Ward (UBC) and the Burnaby school district (Janet Chow): Behavioral Assessment, pEEG brain imaging including pEye-Tracking applied pre/post interventional cognitive training programs in learning diabilities. This pilot project is aimed at understanding how reading ability and word fluency develops and alters in the human brain. Reading is a multi-stage process that incorporates multiple facets of language, including the meaning of words, how they sound, and how they look, among other things. In particular, we are interested in understanding the underlying brain activity that gives rise to student's ability to learn how to read and the underlying mechanisms of remediation following FFW training in poor readers.

  - Bedo, Ender-Fox, Chow, Siegel, Ribary, and Ward. OHBM, 2018.

Developmental Dyslexia - Emotional Impact and Consequences: As PI (with student Emily Livingston-Hirst) and in collaboration with Linda Siegel (UBC), conducted a comprehensive review into current literature, focusing on consequences for the (i) individual, (ii) family and (iii) society, demonstrating the need for further research into high-quality assessment, diagnosis and intervention of dyslexia. The primary and secondary consequences of dyslexia are highly related and therefore suggest multiple avenues of support for academic, emotional, and self-esteem needs, early diagnosis, education and especially including interventions. This review further illustrates and recommends routine screening for dyslexia at early age, including behavioural and brain-imaging research to improve early and accurate diagnostic markers for dyslexia.

  - Hirst, Siegel and Ribary. CNS, 2016.

  - Livingston, Siegel and Ribary. AJLD, 2018.

 

  • Interventional Strategies (Dyslexia)

Collaborative efforts on facilitating the integration of brain-based interventional cognitive programs or Learning Disabilities (Dyslexia) in BC schools: The BCNI Director (BC LEEF Chair Dr.Ribary) is one of the Co-founders (Cairns, Chow, Hernandez, Todd and Ribary) and one of many active Members of the “BC Fast ForWord Intervention Consortium”, a BC school interdistrict strategy to facilitate the knowledge and integration of interventional training programs for Learning Disabilities in BC schools.

Facts: Prior to founding the BC FFW Consortium during the 2007-2008 school year, fewer than 250 students used the FFW intervention in BC schools. Two years later, by the 2009-2010 school year, the number of students enrolled in FFW intervention at BC Consortium schools had increased more than 400%/yr to a total of 1,208 students. As of 2012, the interventional platform has grown to 26 sites with more than 4,000 students successfully enrolled in FFW interventional training in BC over a five-year period, with average training of 43 days, average attendance of 72% and average participation of 92%. Students ranged from Kindergarten through High School, with an average grade level of early 5th grade. 

As of Dec/2014, the interventional FFW training platform has further grown; more than 6,000 students have been trained within 119 schools across 21 districts in BC with an overall gain of 0.7-2.0 years in reading level, including elementary and secondary schools. This is the largest effort across Canada with 51% interventional training in BC alone; i.e. more training in BC than in all the other Provinces combined.

As of Dec/2016, the interventional FFW training platform has further grown; close to a total of 9,000 students have been trained within 130 schools across 22 districts in BC with an overall gain of 0.7-2.0 years in reading level, including elementary and secondary schools. This is by far the largest effort across Canada with 49% training in BC  (AB-26%, ON-8%)

Click link to BC FFW Consortium

2016-present: Expanding efforts together with Mike MacKay (former Superintendant of Surrey), Marlene Lewis (Clinical Psychologist), Sandy Collins and Janet Chow (BC FFW Consortium) to further facilitate the awareness and engagement of cognitive brain-based interventional training programs in BC schools to educators, academics and the public, and the possible exploration of "Intervention Centers for Child-Dyslexia" within the private sector.

  - Ribary and Lewis. Leadership Round-Table with internationally renown educational neuroscientist and author Dr. Martha Burns, Victoria BC, Apr/19/2018.

    (Invitation sent to all School Districts Superintendents across BC, and the BC Ministries)

 

  • Collaboration with Showa University School of Medicine, Tokyo, Japan:

Koiwa and colleagues (Department of Physiology) - Auditory Localization Processing using state-of-the-art dynamic EEG brain imaging analysis:  Application of more advanced data analysis strategies, analyzing time/frequency data plots and differentials on previously recorded EEG data sets across all subjects and all auditory-location conditions with different demands (passive, easy, difficult). Time/frequency data analysis in source space included: (i) beamformer source analysis, (ii) significant activation-locations, (iii) time/frequency analysis of activation within these specified sources, (iiii) connectivity analysis across spatial locations, frequency and time. Outcome: consistent trends and significant new findings consistent with expected neurophysiology and with Koiwa's previous publication, (1) indicating early local primary activation, then (2) formation of more long-range networks, and later (3) formation of more long-range networks and more involvement of non-sensory frontal/parietal areas.

  - Training in state-of-the-art brain imaging data analysis.

 

  • Advancing the analysis of dynamic MEG/EEG brain imaging data:

BCNI's senior scientist Alex Moiseev demonstrated that new data analysis signal processing algorithms provide significant better reconstruction quality than traditional ones. In particular, using simulations and real MEG measurements, he was able to significantly (a) improve source-level SNR and yield more accurately reconstructed time courses; (b) provide more accurate estimates of inter-source correlations; (c) reduce adverse influence of the source correlations. Importantly, these new techniques come at no additional computational cost, but the economic scientific outcome is poised to significantly increase by improving source-based analysis of EEG and MEG data and subsequent local and long-range connectivity and causality measures.

  - Moiseev A, Doesburg SM, Grunau R, and Ribary U. Neuroimage, 2015.

  • Advancing the analysis of brain connectivity dynamics using MEG/EEG:

 BCNI's senior scientist Alex Moiseev and Anthony Herdman (UBC) demonstrated improvement of (a) validating and localizing event-related potentials using multi-source minimum variance beamformers and (b) the source reconstruction in ultra-low SNR conditions for network analysis of resting state data.

  - Herdman AT, Moiseev A, Ribary U. Brain Topography, 2018.

  - Moiseev A and Ribary U. Biomag 2018.

  • Collaboration with Moscow State University of Psychology and Education, Russia:

Tatiana Stroganova (Head of MEG Center in Moscow) and colleagues: Collaborative efforts on training and strategies of analyzing state-of-the-art dynamic brain imaging data of human cognitive processes and their alterations in pathology.

  - Training Anna Baturina (visiting PhD student) for training their Home-Lab personnel.

 

Implementation of real-time MEG (rtMEG) brain imaging:

Implementation of real-time MEG (rtMEG) brain imaging in CTF Systems: Collaboration between BCNI Institute (with senior scientist Alex Moiseev) and CTF , a Vancouver-based MEG manufacturing company. This project generates and tests the prototype for "Real-Time Imaging of Dynamic Brain Activity" on the fly with NO time delay while a subject is scanned. MISL anticipates a significant translational related revenue in their sales by including this real-time system, a huge economic benefit to Canada and further for the basic/clinical research and the healthcare system.

   - Moiseev A, Peatfield N, Doesburg S, Cheung TPL and Ribary U. Biomag, 2016.

 

Collaboration with Fidel Vila-Rodriguez, Psychiatry UBC, and Master student Mina Ekramnia (visiting from Max Planck Institute, Germany): Training and assistance in state-of-the-art EEG brain imaging data analysis strategies for evaluating brain network oscillations and connectivity in medication-resistant depressed patients before and after interventional therapies using TMS (trans magnetic stimulation).

  - Training for Lab personnel; Mina Ekramnia, MA Thesis, UBC, 2016.

Collaboration with Aalto University School of Science, Dept. of Neuroscience and Biomedical Engineering, Espoo, Finland: Risto Ilmoniemi and PhD student Petteri Hyvarinen: Collaborative efforts on novel conceptual and technical state-of-the-art brain imaging data analysis strategies including training, 1) focusing on slowing in resting state and how it affects evoked oscillation dynamics pre/post intervention using a generic head-model, based on their MEG data on tinnitus patients, and 2) testing the BCNI's portable eye-tracker for the possible use on control subjects processing auditory stimuli.

  - Training for Lab personnel; Petteri Hyvarinen, PhD Thesis, Finland, Dec/ 2016.

Engaging in collaborative efforts within the larger multimodal brain imaging community (across SFU, BCCH and UBC), and the publication of a larger comprehensive text-book chapter highlighting the advances in emerging neuroimaging technologies (MRI, fMRI, PET, MEG, EEG, signal processing, visualization, and conceptual scientific frameworks) towards future personalized diagnostics, prognosis, targeted intervention and ethical challenges.

  - Ribary U, Mackay AL, Rauscher A, Tipper CM, Giaschi D, Woodward TS, Sossi V, Doesburg SM, Ward LM, Herdman A, Hamarneh G, Booth BG, and Moiseev A.,

    In: Neuroethics, Illes and Hossain, eds., Oxford University Press, 2017

Other current Projects using BCNI's Infrastructure and Platform (2017-2018)

(PI's: Sam Doesburg and Teresa Cheung)

- Mobile EEG recordings under hypoxic/hypobaric conditions with Victoria Claydon (SFU-BPK) and Sherri Ferguson (SFU);

- Mobile EEG analysis of children with ASD with Grace Iarocci (SFU-Psychology) during ASD summer camp;

- Fostering collaborations between SFU Surrey brain imaging operation and SFU researchers based in Burnaby;

- Integrating computational modeling and neuroimaging methods to develop models of neural systems; extending current dipole equations to quadrupolar

  forms to better model magnetic fields from white matter and spinal cord conduction (with MEG Operation at ImageTech);

- Developing techniques to apply "drizzle" (providing higher resolution) to MEG data (with MEG Operation at ImageTech);

- Exploring OPM magnetometers towardsf building a multichannel system for magnetic spinal cord imaging (with MEG Operation at ImageTech);

- Using median nerve stimulation to examine the feasibility of spinal cord SEP detection using a commercial QuSpin OPM sensor (with MEG Operation at

  ImageTech);

- Developing well-validated and automated data analysis pipelines to improve the clinical efficacy of MEG in surgical planning for epilepsy patients and

  further translating more advanced analysis methods into clinical practice (with MEG Operation at ImageTech);

- Using continuous naturalistic stimuli to better probe complex cognitive and perceptual processes (with MEG Operation at ImageTech);

- Integration of hemodynamic (fNIRS) and electrophysiological (MEG) imaging towards a greater understanding of brain activity (with MEG Operation

  at ImageTech).

BCNI's Infrastructure facilitating many other Research Projects across Disciplines and Institutions:

 

PI Faisal Beg (Co-Director MIAL, Engineering Science SFU):

(a) Summary (2013-2015): The BCNI Institute's infrastructure (i) facilitated the data analysis for over 20-30 lab-members of the MIAL, using more than 16 CPU core years (140'160 hours) and more than 2.25 GPU years (19'710 hours), (ii) enabled a vastly more efficient workflow analyzing ~4,000 MRI and ~3,000 PET images of the brain from SFU-BCCH-UBC and 250 Optical Coherence Tomography (OCT) images of the eye, (iii) resulted in several related journal publications, and (iiii) saved the MIAL more than $30,000.

The BCNI Institute's two high-end computation and visualization servers or “visnodes” (rcg-visnode-01 and rcg-visnode-02) since Fall 2013 has enabled advanced medical image analysis and visualization. Since then, these “visnodes” have been serving as the primary computing resources for over 20-30 members at the Medical Image Analysis Lab (MIAL). The availability of the visnodes with high-end memory and processor specifications (128GB RAM, 12 CPUs cores and 2 GPUs each) allowed researchers to switch to a client-server model for the lab computing setup. In this setup, the old desktops are just used as client terminals to remotely connect to the two visnodes, where the actual medical image processing and related computing tasks are run. The adoption of this new visnodes-based client-server paradigm has saved in individual desktop upgrade costs and has enabled a vastly more efficient workflow due to the use of a central powerful computing resource as opposed to using several less powerful user desktops. In particular, Professor Faisal Beg’s trainees conducting research on the design of computational biomarkers for Alzheimer’s disease from brain and retina imaging scans regularly require the running of image processing algorithms with high memory, multi-core processor and GPU acceleration requirements, which are much above the specifications on a typical user desktop necessitating access to these advanced computational machines. In this context, the availability of the superior computational power on the visnodes is invaluable and is extensively leveraged by Dr. Beg’ lab for the running of resource intensive computations.

The results and findings ensuing from this processing have already resulted in several journal publications with more in progress.

 

BCNI facilitated instrumental Publications (5):

- Raamana, P.R., Weiner, M.W., Wang, L., Beg, M.F., “Thickness Network (ThickNet) features for prognostic applications in dementia”, Neurobiology of Aging, 2014.

- Amanmeet Garg, Darren Wong, Karteek Popuri, Kenneth J. Poskitt, Kevin Fitzpatrick, Bruce Bjornson, Ruth E. Grunau, Mirza Faisal Beg "Manually segmented template library for 8-year-old pediatric brain MRI data with 16 subcortical structures. Journal of Medical Imaging, 1(3), 034502-035412, October, 2014.

- Garg, A., Appel-Cresswell, S., Popuri, K., McKewon, M.J., Beg, M.F, ‘’Morphological alterations in caudate, putamen, palladium, and thalamus in Parkinson’s disease“, Frontiers in Neuroscience, 2015.

- Sieun Lee, Evgeniy Lebed, Marinko Sarunic, Mirza Faisal Beg, "Exact Surface Registration of Retinal Surfaces from 3D Optical Coherence Tomography Images", IEEE Transactions in Biomedical Engineering, 62(2), 609-617, February, 2015.

- Lee, S., Charon, N., Charlier, B., Popuri, K., Lebed, E., Sarunic, M.V., Trouve, A., Beg, M.F., “Atlas-based shape analysis and classification of retinal optical coherence tomography images using the functional shape (fshape) framework”, Medical Image Analysis, 2016, doi.org/10.1016/j.media.2016.08.012.

(b) 2014-2017: PI Faisal Beg received the MIRI Brain Canada Grant, worth 1.5M$ (500k/year) for three years, and the two BCNI viznodes were the main workhorses for all involved students for various interactive work. 16 papers have come out of their work and the PI is appreciative of the BCNI infrastructure for having facilitated in some form or another. In addition, these papers further catalyzed getting the NSERC Discovery accelerator award:

 

BCNI facilitated paper publications (16):

- Morgan Heisler, Sieun Lee, Zaid Mammo, Yifan Jian, Myeong Jin Ju, Andrew Merkur, Eduardo Navajas, Chandrakumar Balaratnasingam, Mirza Faisal Beg, Marinko Sarunic. (2017). Strip-based Registration of Serially Acquired Optical Coherence Tomography Angiography. Journal of Biomedical Optics.

- Sieun Lee, Morgan Heisler, Paul J. Mackenzie, Marinko V. Sarunic, Mirza Faisal Beg. (2017). Quantifying variability in longitudinal peripapillary RNFL and choroidal thickness using surface-based registration of OCT images. Translational Vision Science and Technology.

- Ling Lee, Christine E. Genge, Michelle Cua, Xiaoye Sheng, Kaveh Rayani, Mirza F. Beg, Marinko V. Sarunic, Glen F. Tibbits. (2016). Aortic and Cardiac Structure and Function UsingHigh-Resolution Echocardiography and Optical Coherence Tomography in a MouseModel of Marfan Syndrome. PloS ONE. 11: 1-10.

- Pavle Prentǎsíc ; Morgan Heisler ; Zaid Mammo ; Sieun Lee ; Andrew Merkur ; Eduardo Navajas ; Mirza Faisal Beg ; Marinko Saruníc ; Sven Loňcaríc. (2016). Segmentation of the foveal microvasculature using deep learning networks. Journal of Biomedical Optics. 21(7)

 - Sieun Lee, Nicolas Charon, Benjamin Charlier, Karteek Popuri, Evgeniy Lebed, Marinko Sarunic, Alain Trouvé, Mirza Faisal Beg. (2016). Atlas-based shape analysis and classification of retinal optical coherence tomography images using the functional shape (fshape) framework. Medical Image Analysis. 35: 570-581.

- Zaid Mammo, Morgan Heisler, Chandrakumar Balaratnasingama, Sieun Lee, Dao-Yi Yu, Paul Mackenzie, Steven Schendel, Andrew Merkur, Andrew Kirker, David Albiani, Eduardo Navajas, Mirza Faisal Beg, William Morgan, Marinko V. Sarunic. (2016). Quantitative Optical Coherence Tomography Angiography of Radial Peripapillary Capillaries in Glaucoma, Glaucoma Suspect, and Normal Eyes. American Journal of Ophthalmology. 170: 41-49.

- Ling Lee, Christine E. Genge, Michelle Cua, Xiaoye Sheng, Kaveh Rayani, Mirza F. Beg, Marinko V. Sarunic, Glen F. Tibbits. (2016). Functional assessment of cardiac responses ofadult zebrafish (Danio rerio) to acute and chronic temperature change usinghigh-resolution echocardiography. PloS ONE. 11(1): 1-18.

- Amanmeet Garg, Silke Appel-Cresswell, Karteek Popuri, Martin J McKeown, Mirza Faisal Beg. (2015). Morphological alterations in the caudate, putamen, pallidum, and thalamus in Parkinson's disease. Frontiers in Neuroscience. 9(101): 1-14.

- Eric Lin, Calvin Craig, Marcel Lamothe, Marinko V Sarunic, Mirza Faisal Beg, Glen F Tibbits. (2015). Construction and use of a zebrafish heart voltage and calcium optical mapping system, with integrated electrocardiogram and programmable electrical stimulation. American Journal of Physiology. 308(9): R755- R768.

- Jing Ming, Michael Harms, Matthew Colvin, Mirza Faisal Beg, John Morris, John Csernansky, Lei Wang. (2015). Integrated Cortical Structural Marker for Alzheimer's Disease. Neurobiology of Aging. 36(1): Pages S53–S59.

- Kha Khan AR, Beg MF, Wang L.(2015). Unified Voxel and Tensor-based Morphometry (UVTBM) using Registration Confidence.Neurobiology of Aging. 36(1): S60–S68.

- Mei Young, Sieun Lee, Mahmoud Rateb, Mirza Faisal Beg, Marinko V. Sarunic, Paul J. Mackenzie. (2014). Comparison of the Clinical Disc Margin Seen in Stereo Disc Photographs to Neural Canal Opening Seen in Optical Coherence Tomography Images. Journal of Glaucoma. 26(6): 360-367.

- Weiguang Ding, Eric Lin, Marinko Sarunic, Glen Tibbits, Mirza Faisal Beg. (2014). Automatic Cycle Averaging for Denoising Approximately Periodic Spatiotemporal Signals. IEEE Transactions in Medical Imaging. 33(8): 1749-59.

- Adam Christensen, Kathryn Alpert, Emily Rogalski, Derin Cobia, Julia Rao, Mirza Faisal Beg, Sandra Weintraub, M.-Marsel Mesulam, and Lei Wang. (2014). Hippocampal subfield surface deformity in nonsemantic primary progressive aphasia. Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring. 1(1): 14-23.

- Raamana PR, Wen W, Kochan NA, Brodaty H, Sachdev PS, Wang L, Beg MF.(2014). The sub- classification of amnestic mild cognitive impairment using MRI-based cortical thickness measures.Frontiers in Neurodegeneration. 5(76): 1-10.

- Eric Lin, Amanda Ribeiro, Weiguang Ding, Leif Hove-Madsen, Marinko Sarunic, Mirza Faisal Beg, and Glen Tibbits. (2014). Optical mapping of the electrical activity of isolated adult zebrafish hearts: acute effects of temperature. American Journal of Physiology. 306(11): 823-836.

MEG Operation at SFU-Surrey and Surrey Memorial Hospital:

(a) Users depending on BCNI Infrastructure:

The use of the BCNI infrastructure at SFU Burnaby and the BCNI-access to the merged BCNI-MIAL-FAS computer cluster facilitates many supervisors, staff, postdocs and students.

- Supervisors: Teresa Cheung, Sam Doesburg, Vasily Vakorin, Carolyn Sparrey, Sylvain Moreno, Xiaowei Song, Ryan D’Arcy;

- Post Docs: Nicholas Peatfield;

- Staff: Quan Gao, Pamela Tannori;

- Graduate Students: Sujoy Ghosh-Hajra, Careesa Liu, Shaun Fickling, Matt Courtemanche, Gabby Palowski, Tahira Tejpar, Justine Horne, Adonay Nunes, Nataliia Kozhemiako, Evan Hutcheon;

- Undergraduate Students: Alexandra Talpalaru, Shaquille Nijjer, Anterpal Sandhu, Angela Wen, Tatenda Jakaza, Amneet Mann, Ethan Haid, Sabine Kubler, Carolina Solorzano Barrera, Evangeline Yee, Josh Lu, Daniel Wijaya;

- Summer Students: Luke Conroy and a number of Irish Medical Students and high school students;

Total Number:  35+ at least.

 

(b) Usage of Facilities:

The BCNI Institute facilities have become an important meeting place and work environment for members of the SFU-Surrey lab (about 20km distant from SFU) whenever they are in Burnaby and also remotely from Surrey. Since most educational courses occur on the Burnaby campus, the students find the BCNI space particularly useful when they are at the Burnaby campus for course work. Additionally the space has served as tutorial meeting space for ENSC 461 and a weekly tutorial on MEG data analysis and group lab meetings.

 

 (c) Usage of Cluster Computers:

Lab members from ImageTech and NeuroTech labs and other members of the SFU Surrey Innovation Boulevard initiative have made extensive use of the BCNI servers and disk storage space. Activities include MEG, EEG, MRI, DTI and fMRI data processing and analysis. These activities have expanded recently to include data management and data informatics. These servers are accessed locally using the BCNI computer terminals or remotely through ssh tunnel. Many of the students/postdoc and supervisors are utilizing the BCNI facilities’ computer terminals when they are at SFU Burnaby. As well, the PC based machine running the Presentation stimulus software license has also been utilized to facilitate protocol development. The group members also continue to extensively connect to the servers remotely via ssh tunnel and vnc.

 

 (d) Current and Future Need for BCNI Infrastructure and services:

Without the BCNI infrastructure and the BCNI-related computer cluster, most of the current SFU-Surrey MEG Operation would not be able to process their data, which is critical particularly for the students defending theses. They are grateful for the generous access and are thankful for having a place to meet, interact and build engaging connections.

 

 (e) Multidisciplinary and Inter-Campus Research:

The BCNI is providing a critical meeting space, working space, and computational resources on the Burnaby Campus.  This is key for research collaborations for SFU Surrey-based researchers such as Sam Doesburg, Teresa Cheung and Vasily Vakorin.  This facilitates research collaborations such as those with Grace Iarocci on autism, as well as supporting research using SFU facilities based in both Burnaby and Surrey, such as MEG/MRI brain imaging (Surrey) and hyperbaric physiology (Burnaby).

 

 (f) Facilitating Thesis Defenses:

The BCNI servers and disk storage has been instrumental in processing data for the following successful thesis defenses:

Matt Courtemanche: MASc.; Anterpal Sandhu, BASc, Shaquille Nijjer (BASc).

 

The BCNI Institute facilitated the research of the Multimodal Imaging Operation at SFU-Surrey and Surrey Memorial Hospital, and resulted in 5 published Papers and 27+ Abstracts publications (2014-2017):

- Vakorin VA*, Doesburg SM*, da Costa L, Jetly R, Pang EW, Taylor MJ (2017) Detecting mild traumatic brain injury using resting state magnetoencephalographic network connectivity. PLoS Computational Biology. *These two authors contributed equally to this work.

- Doesburg SM*, Bedo N*, Ward LM (2016) Top-down alpha oscillatory network interactions during visuospatial attention orienting.  NeuroImage. 132:512-519. *These two authors contributed equally to this work.

- Anterpal Sandhu; Yasong Li; Nicholas Peatfield, Xin Yi Yong; Ryan D'Arcy; Carlo Menon; Teresa P L Cheung; “Non-magnetic compliant finger sensor for continuous fine motor movement detection”, Biomedical Engineering Letters (2017).

- Careesa C. Liu1, Sujoy Ghosh Hajra1, Teresa Cheung1,2, Xiaowei Song1,2, Ryan C.N. D’Arcy1,2*, Spontaneous blinks activate the precuneus: Characterizing blink-related oscillations using magnetoencephalography, NeuroImage (2017).

- Li, Y., Yong, X., Cheung, TPL and Menon, C., “Compliant finger sensor for sensorimotor studies in MEG and MR environment”, Smart Materials and Structures, 25 (2016) 075030 (10pp) (2016).

 

BCNI's infrastructure facilitates many other training programs and research projects for SFU-Psychology:

(providing analysis area, conference room, services and equipment)

- BCNI provided space for semesterly Psych 386 EEG Introductory Course (JMD): Introduction to methods and applications for EEG brain imaging and analysis.

- BCNI is the Headquarter for the "Student Society for Behavioral Neuroscience": President LG and executive members are holding weekly meetings at the BCNI.

- BCNI is the Headquarter for the "CNS Graduate Student Journal Club": Organizer EC and members are holding bi-weekly meetings at the BCNI.

- BCNI provided space for several MA and PhD Thesis Defences (Dept. Psychology SFU).

- BCNI provided space for Cognitive Neuroscience Seminars (Dept. Psychology SFU).

- BCNI provides conference room, smartboard and video-conferencing capabilities for regular BCNI Associates Lab-Meetings to discuss and plan their individual research: PI's Grace Iarocci and colleagues, Mario Liotti and colleagues, Tanja Brosch and colleagues, Ralph Mistelberger and colleagues, John McDonald and colleagues, Vince DiLollo, Tom Spalek and colleagues, Marlene Moretti and colleagues, Psych IT Staff, former Cognitive Science Program's Executive Meetings, etc. have used and are continuously using the BCNI space on a regular basis with flexible, independent and user-friendly online bookings.

 

- Demonstration Day on Eye-Tracking from SMI (SensoriMotor Instruments Inc., USA): Introduction, applications and analysis of portable eye-tracker systems on human subjects. SMI is further planning to use the BCNI for a workshop on eye-tracking systems in the fall of 2015, to be presented to SFU at large.

 

September 2018

BCNI - Collaborating to improve the human brain