RESEARCH ACTIVITIES

I am currently an Instructor at the Computational Radiology Laboratory at Children's Hospital Boston, Harvard Medical School.

My research goal is to develop novel medical imaging technologies to improve our understanding of the brain and particularly of brain changes in disease and injuries. My research is driven by the motivation to overcome the current limitations of diffusion-weighted magnetic resonance imaging (DW-MRI) to enable accurate white matter analysis in routine clinical practice. To achieve this goal, I strongly believe that image acquisition and image processing should not be considered separately but conjointly. Therefore, I’m making serious efforts to understand the MR physics underlying the image formation in order to combine both image acquisition advances and novel analysis methods.

I completed an engineering degree in Applied Mathematics and Computer Science in Toulouse University (France), a MS degree in Image Analysis, Vision and Robotics from the Grenoble University (France) and received my Ph.D. degree in Applied Mathematics and Computer Science from Grenoble University in December 2008. During my Ph.D., I focused on anatomical MRI analysis and, more precisely, on brain image segmentation. An important contribution developed in my thesis was the formulation of the notion of ‘collaborative computing’ in a unified and theoretically sound Bayesian framework. This work was awarded by the ``Young Investigator Award’’ at MICCAI’08 in New York and by the ``Best PhD in Applied Mathematics’’ price of INPG Grenoble University in 2009. 

I joined to the Computational Radiology Laboratory (CRL), directed by Dr. Simon K. Warfield in January 2009. I chose to shift my main research focus from anatomic MRI analysis to diffusion-weighted MRI. My research at the CRL has been focusing on novel models to better characterize the brain white matter in DW-MRI and on innovative approaches to increase the spatial resolution of DWI-MRI. My research was awarded by a Trainee Abstract Award at HBM2011, two Magna Cum Laude Merit Award at ISMRM2012 and the Elsevier/MEDIA Best Paper Award 2012.

DOMAIN OF INTEREST

• Diffusion MRI, Anatomical MRI
• Novel MRI acquisitions, Q-space sampling techniques, MRI Physics
• Tissue microstructure imaging, biophysical modeling
• Bayesian Analysis, Markov Random Fields & Image Segmentation.
• Medical & Neuroscience Applications.

SOFTWARE

Friday April 19th, 2013 : MisterI is available! Powerful Medical Image Viewer. Link to web site

PROJECTS

	LOcal and Cooperative Unified Segmentation (LOCUS) In most approaches, tissue and subcortical structure segmentations of MR brain scans are handled globally over the entire brain volume through two relatively independent sequential steps. We investigated a fully Bayesian joint model that integrates within a multi-agent framework local tissue and structure segmentations and local... [more]
	CUbe and SPhere - Multi-Fiber Model diffusion imaging (CUSP-MFM) Parametric and non-parametric models have been proposed to represent the diffusion signal, in order to enable the assessment of white matter connectivity. While it has been widely accepted that a single diffusion tensor provides an excellent parametric representation for an individual white matter fiber bundle, the most appropriate... [more]
	Super-Resolution in Diffusion-Weighted Imaging. Diffusion-weighted imaging (DWI) enables non-invasive investigation and characterization of the white-matter but is strongly limited by the relatively poor resolution achievable. Increasing the resolution in DWI holds out the potential to reveal and investigate novel finer fiber structures not visible with conventional diffusion MRI, and will ... [more]
	Early Predictors and Clinical Correlates of Autism in Tuberous Sclerosis Complex Tuberous Sclerosis Complex (TSC) is a neurocutaneous autosomal dominant disorder involving mutations of the TSC1 or TSC2 genes. It is characterized by the presence of benign tumors throughout the body, including the brain where they are known as cortical tubers. TSC symptoms may take time to develop and vary considerably from ... [more]

SELECTED PUBLICATIONS   [Show All]

Benoit Scherrer, Simon K. Warfield,  Parametric Representation of Multiple White Matter Fascicles from Cube and Sphere Diffusion MRI,  PLoS ONE,  7(11),  2012

Benoit Scherrer, Ali Gholipour, Simon K. Warfield,  Super-resolution reconstruction to increase the spatial resolution of diffusion weighted images from orthogonal anisotropic acquisitions,  Med Imag Analysis,  16(7),  2012,  1465-1476

Elsevier/MEDIA Best Paper Award 2012

Benoit Scherrer, Simon K Warfield,  Why multiple b-values are required for multi-tensor models. Evaluation with a constrained log-Euclidean model,  Proc. of the 7th IEEE International Symposium on Biomedical Imaging (ISBI),  Rotterdam, Netherlands,  2010,  1389-1392

(EN, Draft version)

Benoit Scherrer, Florence Forbes, Catherine Garbay, Michel Dojat,  Distributed Local MRF Models for Tissue and Structure Brain Segmentation,  IEEE Transactions on Medical Imaging,  28(8),  2009,  1278-1295

(EN, Draft version)

Benoit Scherrer, Forbes Forbes, Catherine Garbay, Michel Dojat,  Fully Bayesian Joint Model for MR Brain Scan Tissue and Structure Segmentation,  Proc. of the 11th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI),  11(2),  New-York, USA,  2008,  1066-1074

Young Investigator MICCAI Award in the category Segmentation
(EN, Draft version)

LAST PUBLICATIONS   [Show All]

Benoit Scherrer*, Maxime Taquet*, Simon K. Warfield,  Reliable Selection of the Number of Fascicles in Diffusion Images by Estimation of the Generalization Error,  LNCS (7917),  Asilomar, USA,  2013,  742--753

Benoit Scherrer, Simon K Warfield,  Accurate estimation of a multiple fascicle model is enabled by manipulation of gradient strength in a two-shell HARDI to achieve low TE,  Proc. the 21th International Symposium on Magnetic Resonance in Medicine (ISMRM),  Salt Lake City, USA,  2013

Benoit Scherrer, Maxime Taquet, Onur Afacan, Simon K Warfield,  Does the signal arising from a single fascicle significantly deviates from a monoexponential decay with a clinical scanner?,  Proc. the 21th International Symposium on Magnetic Resonance in Medicine (ISMRM),  Salt Lake City, USA,  2013

Maxime Taquet, Benoit Scherrer, Benoit Macq, Simon K Warfield,  Multi-Fascicle Model Reconstruction from Acquisitions of DWI at a Single B-Value with a Population-Informed Prior,  Proc. the 21th International Symposium on Magnetic Resonance in Medicine (ISMRM),  Salt Lake City, USA,  2013

Onur Afacan, Ali Gholipour, Benoit Scherrer, Simon K Warfield,  Motion Detection for Diffusion Weighted MRI Using EPI Phase Correction Lines,  Proc. the 21th International Symposium on Magnetic Resonance in Medicine (ISMRM),  Salt Lake City, USA,  2013

[All Publications]

HONORS, AWARDS AND GRANTS

2012		Elsevier/MEDIA Best Paper Award 2012 Benoit Scherrer, Ali Gholipour, Simon K. Warfield,  Super-resolution reconstruction to increase the spatial resolution of diffusion weighted images from orthogonal anisotropic acquisitions,  Med Imag Analysis,  16(7),  2012,  1465-1476 Elsevier/MEDIA Best Paper Award 2012 Two Magna Cum Laude Merit Award at ISMRM 2012 (Melbourne, Australia) for the papers: Benoit Scherrer, Mustafa Sahin, Caterina Stamoulis, Sanjay Prabhu, Alireza Akhondi-Asl, Simon K. Warfield,  Globally impaired network of anatomical connectivity in tuberous sclerosis complex patients with autism spectrum disorders,  Proc. the 20th International Symposium on Magnetic Resonance in Medicine (ISMRM),  Melbourne, Australia,  2012 ISMRM Magna Cum Laude Merit Award Benoit Scherrer, Ali Gholipour, Simon K Warfield,  Increasing the resolution of diffusion-weighted MRI with distortion compensated orthogonal acquisitions and super-resolution reconstruction,  Proc. the 20th International Symposium on Magnetic Resonance in Medicine (ISMRM),  Melbourne, Australia,  2012 ISMRM Magna Cum Laude Merit Award IEEE ISBI 2012 Best Paper Award and IEEE ISBI Travel Grant at ISBI Maxime Taquet, Benoit Scherrer, Christopher Benjamin, Sanjay Prabhu, Benoit Macq, Simon K. Warfield,  Interpolating multi-fiber models by Gaussian mixture simplification,  Proc. of the 9th IEEE International Symposium on Biomedical Imaging (ISBI),  Barcelona, Spain,  2012,  928-931 IEEE ISBI 2012 Best Paper Award, IEEE ISBI Travel Grant (EN, Draft version)
2011		Trainee Abstract Award at HBM2011 (Quebec, CA): Benoit Scherrer, Simon K Warfield,  Selecting the number of fibers in a Multi-Fiber Model from CUbe and SPhere (CUSP) Diffusion Imaging,  Proc. of the Human Brain Mapping Conference (HBM),  Quebec, Canada,  2011 Trainee Abstract Award (EN, Draft version)
2009		Applied Mathematics Best PhD Thesis Price Grenoble INP [link]
2008		Student paper award at MICCAI 2008 (New York, USA) in the category "Segmentation" for the paper: Benoit Scherrer, Forbes Forbes, Catherine Garbay, Michel Dojat,  Fully Bayesian Joint Model for MR Brain Scan Tissue and Structure Segmentation,  Proc. of the 11th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI),  11(2),  New-York, USA,  2008,  1066-1074 Young Investigator MICCAI Award in the category Segmentation (EN, Draft version)
2005-2008		Thesis Grant from the French Minister (MENRT Grant)
2007		Third place at the company creation contest organized by "La Maison de l'Entrepreneuriat" Winner of the company creation contest organized during "les DOCTORIALES")
1996, 97, 98		Final of the national programming contest for people under 21 years old Three time among the 100 in the final round (First time: younger finalist, 15years old). Best podium: 26th

MISC

• Reviewer for International Journals
  (Neuroimage, IEEE Transactions on Medical Imaging, IEEE Transactions on Image Processing, IEEE Transactions on Biomedical Engineering)
• Reviewer for International Conferences
  (Medical Imaging Computing and Computer-Assisted Intervention MICCAI)
• Oral session conference co-chair
  ISMRM 2011 (Montreal, CA). Advances in Image Analysis session
  ISBI 2012 (Barcelona, SP). Diffusion Imaging session
  

CURSUS

2008 - PhD in Applied Mathmatics and Computer Science (INPG Grenoble University, France)
2005 - MS degree in Image Analysis, Vision and Robotics (INPG Grenoble University, France)
2004 - ENSEEIHT Engineer in Informatic and Applied Mathematics (Toulouse)