Benoit Scherrer

Benoit Scherrer
Harvard Medical School | HMS · Department of Radiology

Ph.D

About

108
Publications
13,444
Reads
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1,647
Citations
Introduction
My overall research goal is to develop novel medical imaging technologies to improve our understanding of the brain and of brain changes in disease and injuries, with the ultimate objective of impacting clinical decision-making and clinical care.
Additional affiliations
January 2018 - present
Harvard Medical School
Position
  • Professor (Assistant)
December 2012 - January 2018
Harvard Medical School
Position
  • Instructor
January 2009 - December 2012
Boston Children's Hospital
Position
  • Research Associate

Publications

Publications (108)
Article
To develop a statistical model for the tridimensional diffusion MRI signal at each voxel that describes the signal arising from each tissue compartment in each voxel. In prior work, a statistical model of the apparent diffusion coefficient was shown to well-characterize the diffusivity and heterogeneity of the mono-directional diffusion MRI signal....
Article
Diffusion-weighted imaging (DWI) enables non-invasive investigation and characterization of the white matter but suffers from a relatively poor spatial resolution. Increasing the spatial resolution in DWI is challenging with a single-shot EPI acquisition due to the decreased signal-to-noise ratio and T2(∗) relaxation effect amplified with increased...
Article
Full-text available
The characterization of the complex diffusion signal arising from the brain remains an open problem. Many representations focus on characterizing the global shape of the diffusion profile at each voxel and are limited to the assessment of connectivity. In contrast, Multiple Fascicle Models (MFM) seek to represent the contribution from each white ma...
Conference Paper
Full-text available
Models of the diffusion-weighted signal are of strong inter-est for population studies of the brain microstructure. These studies are typically conducted by extracting a scalar property from the model and subjecting it to null hypothesis statistical testing. This process has two major limitations: the reported p-value is a weak predictor of the re-...
Conference Paper
Full-text available
A number of diffusion models have been proposed to overcome the limitations of diffusion tensor imaging (DTI) which cannot represent multiple fascicles with heterogeneous orientations at each voxel. Among them, generative models such as multi-tensor models, CHARMED or NODDI represent each fascicle with a parametric model and are of great interest t...
Article
Background and purpose: Pediatric-onset multiple sclerosis (POMS) shows earlier axonal involvement and greater axonal loss than in adults. We aim to characterize the white matter (WM) microstructural changes in POMS using a diffusion compartment imaging (DCI) model and compare it to standard diffusion tensor imaging (DTI). Methods: Eleven patien...
Article
Full-text available
Psychiatry is undergoing a paradigm shift from the acceptance of distinct diagnoses to a representation of psychiatric illness that crosses diagnostic boundaries. How this transition is supported by a shared neurobiology remains largely unknown. In this study, we first identify single nucleotide polymorphisms (SNPs) associated with psychiatric diso...
Article
Diffusion tensor imaging provides increased sensitivity to microstructural tissue changes compared to conventional anatomical imaging but also presents limited specificity. To tackle this problem, the DIAMOND model subdivides the voxel content into diffusion compartments and draws from diffusion-weighted data to estimate compartmental non-central m...
Article
Objective Approximately 50% of patients with Tuberous Sclerosis Complex develop infantile spasms, a sudden‐onset epilepsy syndrome associated with poor neurological outcomes. While an increased burden of tubers confers an elevated risk of infantile spasms, it remains unknown whether some tuber locations confer higher risk than others. Here, we test...
Article
Full-text available
Background: The right ventricle (RV) often fails when functioning as the systemic ventricle, but the cause is not understood. We tested the hypothesis that myofiber organization is abnormal in the failing systemic right ventricle. Methods: We used diffusion-weighted cardiovascular magnetic resonance imaging to examine 3 failing hearts explanted...
Article
Full-text available
Cross-scanner and cross-protocol variability of diffusion magnetic resonance imaging (dMRI) data are known to be major obstacles in multi-site clinical studies since they limit the ability to aggregate dMRI data and derived measures. Computational algorithms that harmonize the data and minimize such variability are critical to reliably combine data...
Preprint
Full-text available
Diffusion tensor imaging provides increased sensitivity to microstructural tissue changes compared to conventional anatomical imaging but also presents limited specificity. To tackle this problem, the DIAMOND model subdivides the voxel content into diffusion compartments and draws from diffusion-weighted data to estimate compartmental non-central m...
Article
Background: This cohort study utilized diffusion tensor imaging tractography to compare the uncinate fasciculus and inferior longitudinal fasciculus in children with Phelan-McDermid syndrome with age-matched controls and investigated trends between autism spectrum diagnosis and the integrity of the uncinate fasciculus and inferior longitudinal fas...
Article
Full-text available
Background: Autism spectrum disorder (ASD) is prevalent in tuberous sclerosis complex (TSC), occurring in approximately 50% of patients, and is hypothesized to be caused by disruption of neural circuits early in life. Tubers, or benign hamartomas distributed stochastically throughout the brain, are the most conspicuous of TSC neuropathology, but h...
Article
Full-text available
Tuberous sclerosis complex (TSC) is a rare genetic disorder characterized by benign tumors throughout the body; it is generally diagnosed early in life and has a high prevalence of autism spectrum disorder (ASD), making it uniquely valuable in studying the early development of autism, before neuropsychiatric symptoms become apparent. One well-docum...
Article
Full-text available
Reactive microgliosis is an important pathological component of neuroinflammation and has been implicated in a wide range of brain diseases including brain tumors, multiple sclerosis, Parkinson's disease, Alzheimer's disease, and schizophrenia. Mapping reactive microglia in-vivo is often performed with PET scanning whose resolution, cost, and avail...
Article
Full-text available
Diffusion-weighted magnetic resonance imaging (dMRI) is widely used to infer microstructural characteristics of tissue, particularly in cerebral white matter. Histological validation of the metrics derived from dMRI methods are needed to fully characterize their ability to capture biologically-relevant histological features non-invasively. The data...
Article
Full-text available
Background: Multi-site MRI studies are often necessary for recruiting sufficiently sized samples when studying rare conditions. However, they require pooling data from multiple scanners into a single data set, and therefore it is critical to evaluate the variability of quantitative MRI measures within and across scanners used in multi-site studies...
Article
Micro-architectural characteristics of white matter can be inferred through analysis of diffusion-weighted magnetic resonance imaging (dMRI). The diffusion-dependent signal can be analyzed through several methods, with the tensor model being the most frequently used due to its straightforward interpretation and low requirements for acquisition para...
Article
Full-text available
Objective: Diffusion tensor imaging (DTI) of the white matter is a biomarker for neurological disease burden in tuberous sclerosis complex (TSC). To clarify the basis of abnormal diffusion in TSC, we correlated ex vivo high-resolution diffusion imaging with histopathology in four tissue types: cortex, tuber, perituber, and white matter. Methods:...
Article
Purpose: Electrical source imaging may yield ambiguous results in multilesional epilepsy. The aim of this study was to test the clinical utility of lesion-constrained electrical source imaging in epilepsy surgery in children with tuberous sclerosis complex. Methods: Lesion-constrained electrical source imaging is a novel method based on a propos...
Chapter
We present a summary of competition results in the multi-shell diffusion MRI harmonisation and enhancement challenge (MUSHAC). MUSHAC is an open competition intended to stimulate the development of computational methods that reduce scanner- and protocol-related variabilities in multi-shell diffusion MRI data across multi-site studies. Twelve differ...
Preprint
Full-text available
Micro-architectural characteristics of white matter can be inferred through analysis of diffusion-weighted magnetic resonance imaging (dMRI). The diffusion-dependent signal can be analyzed through several methods, with the tensor model being the most frequently used due to its straightforward interpretation and relaxed acquisition parameters. While...
Article
Purpose To achieve motion‐robust diffusion compartment imaging (DCI) in near continuously moving subjects based on simultaneous multi‐slice, diffusion‐weighted brain MRI. Methods Simultaneous multi‐slice (SMS) acquisition enables fast and dense sampling of k‐ and q‐space. We propose to achieve motion‐robust DCI via slice‐level motion correction by...
Article
After initially successful treatment of infantile spasms, the long-term cumulative risk of relapse approaches 50%, and there is no established protocol to mitigate this risk. Although vigabatrin may be an effective means to prevent relapse, there is little guidance as to ideal duration and dosage. Using a cohort of children with infantile spasms an...
Article
Objective: We studied the longitudinal effects of everolimus, an inhibitor of the mammalian target of rapamycin (mTOR), on callosal white matter diffusion tensor imaging (DTI) in patients with tuberous sclerosis complex (TSC). Methods: Serial imaging data spanning nine years were used from the open label, Phase I/II trial (NCT00411619) and open-...
Article
Objective: Phelan-McDermid syndrome is caused by haploinsufficiency of SHANK3 on terminal chromosome 22. Knowledge about altered neuroanatomic circuitry in Phelan-McDermid syndrome comes from mouse models showing striatal hypertrophy in the basal ganglia, and from humans with evidence of cerebellar atrophy. To date, no studies have performed volum...
Article
Many closed-form analytical models have been proposed to relate the diffusion-weighted magnetic resonance imaging (DW-MRI) signal to microstructural features of white matter tissues. These models generally make assumptions about the tissue and the diffusion processes which often depart from the biophysical reality, limiting their reliability and in...
Article
Objective: In this cohort analysis, we studied 1-year-old infants with tuberous sclerosis complex (TSC), correlating volumes of cerebellar structures with neurodevelopmental measures. Methods: We analyzed data from a prospective biomarker study in infants with TSC (ClinicalTrials.gov NCT01780441). We included participants aged 12 months with an...
Article
Full-text available
This technical innovation describes the development of a novel device to aid technologists in reducing exposure variation and repeat imaging in computed and digital radiography. The device consists of a color video and depth camera in combination with proprietary software and user interface. A monitor in the x-ray control room displays the position...
Article
Introduction: Neurological manifestations in Tuberous Sclerosis Complex (TSC) are highly variable. Diffusion tensor imaging (DTI) may reflect the neurological disease burden. We analyzed the association of autism spectrum disorder (ASD), intellectual disability (ID) and epilepsy with callosal DTI metrics in subjects with and without TSC. Methods:...
Article
Preterm birth disrupts and alters the complex developmental processes in the cerebral cortex. This disruption may be a contributing factor to widespread delay and cognitive difficulties in the preterm population. Diffusion-weighted magnetic resonance imaging (DW MRI) is a noninvasive imaging technique that makes inferences about cellular structures...
Article
The Insight Toolkit (ITK) utilizes a generic design for image processing filters that allows many developers to rapidly implement new algorithms. While ITK filters benefit from a platform-independent and versatile multithreading capability, the current implementation does not easily achieve high performance. First, ITK relies on a static decomposit...
Article
Full-text available
Purpose: To assess the validity of the superposition approximation for crossing fascicles, i.e., the assumption that the total diffusion-weighted MRI signal is the sum of the signals arising from each fascicle independently, even when the fascicles intermingle in a voxel. Methods: Monte Carlo simulations were used to study the impact of the appr...
Article
Full-text available
A large number of mathematical models have been proposed to describe the measured signal in diffusion-weighted (DW) magnetic resonance imaging (MRI). However, model comparison to date focuses only on specific subclasses, e.g. compartment models or signal models, and little or no information is available in the literature on how performance varies a...
Conference Paper
Diffusion compartment imaging (DCI) characterizes tissues in vivo by separately modeling the diffusion signal arising from a finite number of large scale microstructural environments in each voxel, also referred to as compartments. The DIAMOND model has recently been proposed to characterize the 3-D diffusivity of each compartment using a statistic...
Article
Diffusion weighted magnetic resonance imaging, or DWI, is one of the most promising tools for the analysis of neural microstructure and the structural connectome of the human brain. The application of DWI to map early development of the human connectome in-utero, however, is challenged by intermittent fetal and maternal motion that disrupts the spa...
Article
By shortening the acquisition time of MRI, Echo Planar Imaging (EPI) enables the acqui- sition of a large number of images in a short time, com- patible with clinical constraints as required for diffusion or functional MRI. However such images are subject to large, local distortions disrupting their correspondence with the underlying anatomy. The c...
Conference Paper
Simultaneous multi-slice (SMS) echo-planar imaging has had a huge impact on the acceleration and routine use of diffusion-weighted MRI (DWI) in neuroimaging studies in particular the human connectome project; but also holds the potential to facilitate DWI of moving subjects, as proposed by the new technique developed in this paper. We present a nov...
Article
This work proposes a novel approach for motion-robust diffusion-weighted (DW) brain MRI reconstruction through tracking temporal head motion using slice-to-volume registration. The slice-level motion is estimated through a filtering approach that allows tracking the head motion during the scan and correcting for out-of-plane inconsistency in the ac...
Article
Streamline tractography algorithms infer connectivity from diffusion MRI (dMRI) by following diffusion directions which are similarly aligned between neighboring voxels. However, not all white matter (WM) fascicles are organized in this manner. For example, Meyer's loop is a highly curved portion of the optic radiation (OR) that exhibits a narrow t...
Article
Modern medical imaging makes use of high performance computing to accelerate image acquisition, image reconstruction, image visualization and image analysis. Software libraries that provide implementations of key medical imaging algorithms need to efficiently exploit modern CPU architectures. In particular, workstations with small numbers of cores...
Article
Purpose:To determine the feasibility of using a computer vision algorithm and augmented reality interface to reduce repeat rates and improve consistency of image quality and patient exposure in general radiography. Methods:A prototype device, designed for use with commercially available hardware (Microsoft Kinect 2.0) capable of depth sensing and h...
Conference Paper
Full-text available
Synopsis The DIAMOND model has been recently proposed to model the heterogeneity of tissue compartments in diffusion compartment imaging. However, it did not enable the characterization of the intra-axonal volume fraction (IAVF), a critical measure to more accurately characterizing axonal loss in abnormal tissues. In this work we investigated mathe...
Article
Purpose: To compare and evaluate the use of super-resolution reconstruction (SRR), in frequency, image, and wavelet domains, to reduce through-plane partial voluming effects in magnetic resonance imaging.
Article
Objective: To assess the extent and evolution of tissue abnormality of tubers, perituber tissue, and normal-appearing white matter (NAWM) in patients with tuberous sclerosis complex using serial diffusion tensor imaging. Methods: We applied automatic segmentation based on a combined global-local intensity mixture model of 3T structural and 35 di...
Article
PurposeTo develop a statistical model for the tridimensional diffusion MRI signal at each voxel that describes the signal arising from each tissue compartment in each voxel.Theory and Methods In prior work, a statistical model of the apparent diffusion coefficient was shown to well-characterize the diffusivity and heterogeneity of the mono-directio...
Conference Paper
Full-text available
Acquisition of a series of anisotropically oversampled acquisitions (so-called anisotropic "snapshots") and reconstruction in the image space has recently been proposed to increase the spatial resolution in diffusion weighted imaging (DWI), providing a theoretical 8x acceleration at equal signal-to-noise ratio (SNR) compared to conventional dense k...
Article
Full-text available
We introduce a new approach to correct geometric and intensity distortion of Echo Planar Images (EPI) from images acquired with opposite phase encoding directions. A new symmetric block-matching registration algorithm has been developed for this purpose relying on new adapted transformations between blocks and a symmetric optimization scheme to ens...
Article
The hippocampus and the insula are responsible for episodic memory formation and retrieval. Hence, visualization of the cytoarchitecture of such structures is of primary importance to understand the underpinnings of conscious experience. Magnetic Resonance Imaging (MRI) offers an opportunity to non-invasively image these crucial structures. However...
Article
Diffusion-weighted magnetic resonance imaging (DW-MRI) provides a novel insight into the brain to facilitate our understanding of the brain connectivity and microstructure. While in-vivo DW-MRI enables imaging of living patients and longitudinal studies of brain changes, post-mortem ex-vivo DW-MRI has numerous advantages. Ex-vivo imaging benefits f...
Article
Full-text available
The brain microstructure consists of the complex organization of cellular structures and extra-cellular space. Insights into this microstructure can be gained in vivo by means of diffusion-weighted imaging that is sensitive to the local patterns of diffusion of water molecules throughout the brain. Diffusion compartment imaging (DCI) provides a sep...
Conference Paper
Full-text available
Models of the diffusion-weighted signal are of strong interest for population studies of the brain microstructure. These studies are typically conducted by extracting a scalar property from the model and subjecting it to null hypothesis significance testing. This process has two major limitations: the reported p-value is a weak predictor of the rep...