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Publications and Presentations
Peer-Reviewed Journal Publications
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Fabiola Bezerra de Carvalho Macruz, Charles Lu, Julia Strout, Angelo Takigami, Rupert Brooks,
Sean Doyle, Min Yun, Varun Buch, Sandeep Hedgire, and Brian Ghoshhajra. 2022.
Quantification of the Thoracic Aorta and Detection of Aneurysm at CT: Validation of
a Fully Automatic Methodology.
Radiology: Artificial Intelligence. 4(2)DOI:
10.1148/ryai.210076
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Amiri, M., Brooks, R., Rivaz, H. 2020.
Fine-tuning U-Net for ultrasound image segmentation: different layers, different
outcomes.
IEEE Trans. on Ultrasonics, Ferroelectrics and Frequency Control. DOI: 10.1109/TUFFC.2020.3015081
pdf, supplementary material
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Amiri, M., Brooks, R., Behboodi, B., Rivaz, H. 2020.
Two stage ultrasound image segmentation using U-Net and test time augmentation
International Journal of Computer Assisted Radiology and Surgery. DOI: 10.1007/s11548-020-02158-3
pdf
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Shams, R., Xiao, Y., Hebert, F., Abramowitz, M., Brooks, R., Rivaz, H. 2018.
Assessment of Rigid Registration Quality Measures in Ultrasound-Guided Radiotherapy
IEEE Transactions on Medical Imaging. Vol. 37, No. 2, pp. 428-437. DOI: 10.1109/TMI.2017.2755695 pdf
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Neubauer, A., Brooks, R., Brouwer, I., Debergue, P., Laroche, D. 2013.
Haptic collision handling for simulation of transnasal surgery.
Computer Animation and Virtual Worlds, Vol. 24, No. 2, pp. 127-141. DOI: 10.1002/cav.1489.
http://onlinelibrary.wiley.com/doi/10.1002/cav.1489/abstract
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Clarke, D. B., D'Arcy, R. C. N, Delorme, S., Laroche, D., Godin, G., Ghosh Hajra, S., Brooks, R.,
DiRaddo, R. 2012.
"Virtual Reality Simulator: Demonstrated Use in Neurosurgical Oncology."
Surgical Innovation, Vol. 20, No. 2, pp. 190-197. (April 2013). Prepublished June 20, 2012 as
doi:10.1177/1553350612451354.
http://sri.sagepub.com/content/20/2/190.abstract
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Brooks, R., Arbel, T. 2010.
"Generalizing Inverse Compositional and
ESM Image Alignment."
International Journal of Computer Vision,
Vol. 87, No. 3, pp. 191-212
http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s11263-009-0263-8
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Brooks, R., Arbel, T., Precup, D. 2008.
"Anytime
similarity measures for faster alignment."
Computer
Vision and Image Understanding, Vol. 110, No. 3, pp. 378-389.
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Peer-Reviewed Conference Publications
J. P. Cohen, J. D. Viviano, P. Bertin, P. Morrison, P. Torabian, M. Guarrera, M. P. Lungren, A.
Chaudhari, R. Brooks, M. Hashir, H. Bertrand.
TorchXRayVision: A library of chest X-ray datasets and models.
Proceedings of the Fifth Conference on Medical Imaging with Deep Learning. 2022.
https://2022.midl.io/papers/d_l_7 and
https://github.com/mlmed/torchxrayvision
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J. P. Cohen, R. Brooks, S. En, E. Zucker, A. Pareek, M. Lungren, A. Chaudhari.
Gifsplanation via Latent Shift: A Simple Autoencoder Approach
to Counterfactual Generation for Chest X-Rays.
Proceedings of the Fourth Conference on Medical Imaging with Deep Learning, PMLR 143:74-104. 2021.
https://proceedings.mlr.press/v143/cohen21a.html
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J. P. Cohen, M. Hashir, R. Brooks and H. Bertrand.
On the limits of cross-domain generalization in automated X-ray prediction.
Medical Imaging and Deep Learning 2020.
Paper on MIDL. https://arxiv.org/abs/2002.02497
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B. Behboodi, M. Fortin, C. J.Belasso, R. Brooks, and H. Rivaz.
Receptive Field Size as a Key Design Parameter for Ultrasound Image Segmentation
with U-Net.
. IEEE EMBC, 2020, https://ieeexplore.ieee.org/document/9175846
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B. Behboodi, M. Amiri*, R. Brooks, H. Rivaz.
Breast lesion segmentation in ultrasound images with limited annotation data.
, IEEE ISBI 2020, pp 1834-1837
pdf link. https://arxiv.org/abs/2001.07322
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M. Amiri, R. Brooks, H. Rivaz.
Fine tuning U-Net for ultrasound image segmentation: which layers?
, MICCAI MIL3ID Workshop, 2019, pp 235-242
Springer, pdf link. https://arxiv.org/abs/2002.08438
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Jen-Tang Lu, Rupert Brooks, Stefan Hahn, Jin Chen, Varun Buch, Gopal Kotecha, Katherine P.
Andriole, Brian Ghoshhajra, Joel Pinto, Paul Vozila, Mark Michalski, Neil A. Tenenholtz.
DeepAAA: clinically applicable and generalizable detection of abdominal aortic
aneurysm using deep learning
In Proceedings of the 22nd International Conference on Medical Image Computing and Computer Assisted
Intervention (MICCAI 2019). Oct. 13-17, 2019. Shenzhen, China. Arxiv Preprint:
https://arxiv.org/abs/1907.02567
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Jen-Tang Lu, Rupert Brooks, Varun Buch, Ryan King, Stefan Hahn, Jin Chen, Gopal Kotecha, Bernardo
C. Bizzo, Katherine P. Andriole, Joel Pinto, Brian Ghoshhajra, Mark H. Michalski
DeepAAA: Automated Detection of Abdominal Aortic Aneurysms using Deep Learning.
In Society for Imaging Informatics in Medicine conference 2019. (SIIM'19) June 26-28, 2019. Aurora, CO,
USA.
https://cdn.ymaws.com/siim.org/resource/resmgr/siim2019/abstracts/ML_Abdomen_Chest_Lu.pdf
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Gueziri, H.-E., Tremblay, S., Laporte, C. and Brooks, R.
Graph-based 3D-Ultrasound reconstruction of the liver in the presence of respiratory
motion.
In MICCAI workshop on Reconstruction and Analysis of Moving Body Organs (RAMBO) 2016. Athens,
Greece.
(Researchgate PDF)
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Pishdad, L. and Brooks, R.
Prediction of respiratory motion.
In Electronic Portal Imaging 2016 (EPI2K16). St. Louis, Missouri.
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Abramowitz, M. C., Bossart, E., Flook, R., Wu, X., Brooks, R., Lachaine, M., Lathuiliere, F., Wu,
X., Pollack, A.
Noninvasive Real-time Prostate Tracking Using a Transperineal Ultrasound Approach
International journal of radiation oncology, biology, physics 1 November 2012 (volume 84 issue 3 Page
S133 DOI: 10.1016/j.ijrobp.2012.07.145) (Proceedings of 54th ASTRO.) http://dx.doi.org/10.1016/j.ijrobp.2012.07.145
Talk: http://www.americanradiumsociety.org/noninvasive-real-time-prostate-tracking-using-a-transperineal-ultrasound-approach/
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Brooks, R.
Intrafraction prostate motion correction using a non-rectilinear image frame
, in Madabhushi, A. et. al, (Eds.):Proceedings of the International Workshop on Prostate Cancer
Imaging. Image Analysis and Image-Guided Interventions, in conjunction with MICCAI 2011. Toronto,
Canada, Sept. 22, 2011.
http://www.springerlink.com/content/978-3-642-23943-4/#section=963296&page=1&locus=0
Unfortunately, a formula in this paper has an error, the corrected formula is in the poster from the conference.
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Clarke, D., Brooks, R., D'Arcy, R., Jiang, D., Ayres, F., Ghosh-Hajra, S.,
Stevens, T., Hovdebo, J., Borgeat, L., Massicotte, P., Poirier, G., Mora, V., Marcotte, J-P., Laroche,
D., Delorme, S., Diraddo, R.
World's first patient-specific open neurosurgery rehearsal
,
in Canadian Neurological Sciences Federation Annual Congress, Québec, Québec, Canada. June
8, 2010.
http://nparc.cisti.nrc.ca/npsi/ctrl?action=shwart&index=an&req=16907866&lang=en
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Fan, S., Brooks, R., Ferrie, F.
Better Correspondence by Registration
, in Proceedings of the 9th Asian Conference on Computer Vision,
Xi'an, China, Sept. 2009.
http://www.springerlink.com/content/w781701323471480/
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Mora, V., Jiang, D., Brooks, R., and Delorme, S.
A Computer Model of Soft Tissue Interaction
with a Surgical Aspirator
,
in G.-Z. Yang et al. (Eds.):
Proceedings of the 12th International Conference on Medical Image Computing and Computer Assisted
Intervention (MICCAI 2009), Part I, LNCS 5761, pp. 51�58, London, UK, Sept. 2009.http://www.springerlink.com/content/b66wxp3q135p1534/,
or http://nparc.cisti.nrc.ca/npsi/ctrl?action=shwart&index=an&req=18397768&lang=en
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Audette, M., Brooks, R., Funnell, R., Strauss, G. and Arbel, T.
Piecewise affine initialized spline-based patient-specific registration of a
high-resolution ear model for surgical guidance
, in Proceedings of the MICCAI 2008 Workshop on Image Guidance and Computer Assistance for
Soft-Tissue Interventions, New York, U.S.A., Sept. 2008 https://www.researchgate.net/publication/228918573_Piecewise_affine_initialized_spline-based_patient-specific_registration_of_a_high-resolution_ear_model_for_surgical_guidance
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Brooks, R., Collins, D. L., Morandi, X. and Arbel, T.
Deformable ultrasound registration without reconstruction
, in Proceedings of the 11th International Conference on Medical Image Computing and Computer
Assisted Intervention, New York, U.S.A., Sept. 2008.
http://www.springerlink.com/content/b1110wg8627607h2/
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Brooks, R., Arbel, T. 2007.
The Importance of Scale When Selecting Pixels for Image Registration.
Proceedings of the 4th Canadian Conference on Computer and Robot Vision (CRV). pp. 235-242.
Montreal, Canada. May 2007. http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=4228544
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Brooks, R., Arbel, T., Precup, D. 2007.
Fast Image Alignment Using Anytime Algorithms.
Proceedings of the 20th International Joint Conference on Artificial Intelligence (IJCAI). pp
2078-2083. Hyderabad, India. Jan. 2007. http://www.ijcai.org/papers07/Papers/IJCAI07-335.pdf
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Brooks, R., Arbel, T. 2006.
Generalizing inverse compositional image alignment.
Proceedings of the 18th International Conference on Pattern Recognition (ICPR) Vol. 2, pp.
1200-1203. Hong Kong, China. Aug. 2006. http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=1699424
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Brooks, R., Collins, D. L., Arbel, T. 2005.
Scaling angles and distances to maximize efficiency of image registration
Medical Image Computing and Computer Aided Intervention (MICCAI) 2005 short paper. Palm Springs,
USA, Oct. 2005. http://www.ia.unc.edu/MICCAI2005/ShortPapers/
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Laporte, C., Brooks, R., Arbel, T. 2004.
A fast discriminant approach to active object recognition and pose estimation.
Proceedings of the 17th International Conference on Pattern Recognition, Cambridge, United Kingdom,
Aug. 2004.http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=1334476
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Brooks, R., Harvey, K. D., Kirk, D. W., Soulard, F., Murray, A., Paul, P. 2002.
Building A Canadian Digital Drainage Areas Framework
55th Annual CWRA Conference, Winnipeg, Manitoba, Canada, June 14, 2002.
http://www.rupertbrooks.ca/downloads/Drainage_Area_Framework.pdf
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Thomson, Robert and Brooks, Rupert. 2002.
Exploiting Perceptual Grouping For Map Analysis, Understanding And
Generalization: The Case Of Road And River Networks.
In D. Blostein and Y. B. Kwon (eds.) Graphics Recognition: Algorithms and Applications (Lecture
Notes in Computer Science, vol. 2390), pages 141-150, Springer, Berlin, 2002. This is a revised version
of the paper below.http://www.springerlink.com/content/b3dhemmnqr2wu5yt/
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Thomson, Robert and Brooks, Rupert. 2001.
Exploiting Perceptual Grouping For Map Analysis, Understanding And
Generalization: The Case Of Road And River Networks.
Graphic Recognition 2001, Queens University, Kingston Ontario Canada, September 2001. This paper
was revised and published in LNCS - see the above reference.
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Brooks, R., Dussault, C., Chorlton, L. 1999.
POSTER: Automatic Generalization of Multiclassed Area Patches.
The 19th International Cartographic Conference, ICA99. Ottawa, Ontario, Canada, August 1999.
http://www.rupertbrooks.ca/downloads/icagenposter.pdf (8 Megabytes)
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Brooks, R. 1999.
The New and Improved Base Framework For National Atlas Data
The 19th International Cartographic Conference, ICA99. Ottawa, Ontario, Canada, August 1999. http://atlas.gc.ca/english/about_us/index_pres_e.html#framework
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Coleman, D. J. and Brooks, R. 1995.
Applying Collaborative Production Approaches to GIS Data Collection and Electronic
Chart Production
NCGIA Research Initiative 17: Collaborative Spatial Decision Making. Santa Barbara, California,
USA, September 1995. http://www.ncgia.ucsb.edu/research/i17/htmlpapers/coleman/Coleman.html
Ph.D. Thesis
Brooks, R.
Efficient and Reliable Methods for Direct
Parameterized Image Registration
. McGill University, September 2008.
http://www.rupertbrooks.ca/downloads/Brooks_PhDThesis.pdf
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Patents and Patent Applications
Brooks, R., Moreau, M., Pishdad, L. 2016.
Therapy control using motion prediction based on cyclic motion model.
U.S. Patent No. 10300303B2. Priority date Jan. 29, 2016. https://patents.google.com/patent/US10300303B2/en.
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Pishdad, L., Brooks, R. 2016.
Therapy control using motion prediction.
U.S. Patent No. 10293184B2. Priority date Jan. 29, 2016. https://patents.google.com/patent/US10293184B2/en.
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Brooks, R. 2015.
System and method for target tracking using a quality indicator during radiation
therapy.
U.S. Patent No. US10350438B2. Priority date Jun. 30, 2015. https://patents.google.com/patent/US10350438B2/en.
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Book Chapters
Thomson, R., Brooks, R. 2007.
Generalisation of Geographic Networks.
In Mackaness, W., Ruas, A. and Sarjakoski, L. (Eds). Generalisation of Geographic Information:
Cartographic Modelling and Applications. Chapter 13. Elsevier. http://www.elsevier.com/wps/find/bookdescription.cws_home/711470/description.
Other Publications
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Parisa Kaviani, Mannudeep K. Kalra, Subba R Digumarthy, Karen Rodriguez, Sheela Agarwal,
Rupert Brooks, Sovann En, Tarik Alkasab, Bernardo C. Bizzo, Keith J. Dreyer.
2024.
Artificial intelligence-generated smart impression from 9.8-million radiology
reports as training datasets from multiple sites and imaging modalities
medRxiv 2024.03.07.24303787; doi:
https://doi.org/10.1101/2024.03.07.24303787
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Brooks, R. 2011.
A Gradient Descent Trust Region Optimizer
Insight Journal. IJ-2011 June-December Issue. http://hdl.handle.net/10380/3310
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Brooks, R., Arbel, T. 2007.
Improving The Oriented Image Class For Use In The Registration Framework
Insight Journal. IJ-2007 June-December Issue. http://hdl.handle.net/1926/1293
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Brooks, R., Arbel, T. 2007.
A Homogeneous Transform Class for the ITK.
Insight Journal. IJ-2007 January-June Issue. http://hdl.handle.net/1926/493
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Brooks, R., Arbel, T. 2007.
Improvements to the itk::KernelTransform and Subclasses.
Insight Journal. IJ-2007 January-June. http://hdl.handle.net/1926/494
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Brooks, R. 2002.
Open Sourcing Generalization Tools
ISPRS / SDH Workshop on Multiscale Spatial Data, Ottawa, Ontario, Canada, July 7, 2002. http://www.rupertbrooks.ca/downloads/open_sourcing.pdf
(17 Megabytes)
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Brooks, R. 2002.
The ABCs of GIS.
AAFC GISIM/IT Symposium, St. Ad�le, Qu�bec, Canada, June 4, 2002.
http://www.rupertbrooks.ca/downloads/ABCs_of_GIS_V1.1.zip (zipped powerpoint - 3 Megabytes)
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Brooks, R., Chen, J., Nussbaum, D., Sack, J.-R. 2002.
POSTER: A Parallel Displacement Operator.
4th GEOIDE Annual
Conference. Toronto, Ontario, Canada, May 2002.
http://www.ruperbrooks.ca/downloads/displace.pdf (6.5 Megabytes)
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Brooks, R. 2001.
A "Seat of the Pants" Displacement Operator.
Dagstuhl Seminar 01191: Computational Cartography and Spatial Modelling. Wadern, Germany, May 2001.
http://www.rupertbrooks.ca/downloads/pres_displacement_dagstuhl.pdf
(5 Megabytes)
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Brooks, Rupert. 2000.
National Atlas of Canada Producing First Map Using Automated Generalisation of
Framework Data.
Cartouche, Number 39, Fall 2000.
http://www.rupertbrooks.ca/downloads/northernmap_cartouche.pdf
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Thomson, Robert and Brooks, Rupert. 2000.
Efficient Generalisation and Abstraction of Network Data Using Perceptual Grouping.
5th International Conference on Geocomputation. University of Greenwich, Medway, UK. August 2000.
http://www.geocomputation.org/2000/GC029/Gc029.htm
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Brooks, R. 2000.
Two Birds with one Stone: Constructing National Framework Data for the Global Map.
Global Mapping Forum 2000. Hiroshima, Japan, November 2000.
http://www.iscgm.org/more-iscgm/forum2000/MrRupertBrooks.pdf
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Brooks, R., Evans, R. 1999.
Feasibility of Using Automated Generalisation Techniques to Process the National
Road Network.
Technical Report. GeoAccess Division, Canada Centre for Remote Sensing, Natural Resources Canada
http://www.rupertbrooks.ca/downloads/roads_master.pdf (7 Megabytes)
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Last modified: Wed May 16 2018
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