Benjamin De Leener | École Polytechnique de Montréal (original) (raw)
Papers by Benjamin De Leener
Neurosurgery, 2016
Diffusion tensor imaging (DTI), magnetization transfer (MT), and T2*-weighted imaging measure asp... more Diffusion tensor imaging (DTI), magnetization transfer (MT), and T2*-weighted imaging measure aspects of spinal cord microstructure. This study investigates if these techniques can quantify injury to individual white matter (WM) tracts and correlate with focal neurological impairments in degenerative cervical myelopathy (DCM). Fifty-seven DCM patients (age 56.7; 61% male; 32 mild, 16 moderate, 9 severe) underwent comprehensive clinical assessments and multimodal MRI (3T GE). Analysis with Spinal Cord Toolbox extracted fractional anisotropy (FA), MT ratio (MTR), and T2* WM/gray matter (GM) ratio (representing gray-white contrast) from regions of interest including: total WM, lateral corticospinal tracts (LCSTs), dorsal columns (DCs), and spinothalamic tracts (STTs) at C1-C2. Spearman correlations were calculated between total WM and global disability (mJOA), and between metrics in unilateral/bilateral WM tracts and measures of focal neurological impairment: mJOA upper/lower extremity...
GigaScience, 2016
Brainhack events offer a novel workshop format with participant-generated content that caters to ... more Brainhack events offer a novel workshop format with participant-generated content that caters to the rapidly growing open neuroscience community. Including components from hackathons and unconferences, as well as parallel educational sessions, Brainhack fosters novel collaborations around the interests of its attendees. Here we provide an overview of its structure, past events, and example projects. Additionally, we outline current innovations such as regional events and post-conference publications. Through introducing Brainhack to the wider neuroscience community, we hope to provide a unique conference format that promotes the features of collaborative, open science.
Magnetic Resonance Materials in Physics, Biology and Medicine, 2016
Segmenting the spinal cord contour is a necessary step for quantifying spinal cord atrophy in var... more Segmenting the spinal cord contour is a necessary step for quantifying spinal cord atrophy in various diseases. Delineating gray matter (GM) and white matter (WM) is also useful for quantifying GM atrophy or for extracting multiparametric MRI metrics into specific WM tracts. Spinal cord segmentation in clinical research is not as developed as brain segmentation, however with the substantial improvement of MR sequences adapted to spinal cord MR investigations, the field of spinal cord MR segmentation has advanced greatly within the last decade. Segmentation techniques with variable accuracy and degree of complexity have been developed and reported in the literature. In this paper, we review some of the existing methods for cord and WM/GM segmentation, including intensity-based, surface-based, and image-based methods. We also provide recommendations for validating spinal cord segmentation techniques, as it is important to understand the intrinsic characteristics of the methods and to evaluate their performance and limitations. Lastly, we illustrate some applications in the healthy and pathological spinal cord. One conclusion of this review is that robust and automatic segmentation is clinically relevant, as it would allow for longitudinal and group studies free from user bias as well as reproducible multicentric studies in large populations, thereby helping to further our understanding of the spinal cord pathophysiology and to develop new criteria for early detection of subclinical evolution for prognosis prediction and for patient management. Another conclusion is that at the present time, no single method adequately segments the cord and its substructure in all the cases encountered (abnormal intensities, loss of contrast, deformation of the cord, etc.). A combination of different approaches is thus advised for future developments, along with the introduction of probabilistic shape models. Maturation of standardized frameworks, multiplatform availability, inclusion in large suite and data sharing would also ultimately benefit to the community.
NeuroImage: Clinical, 2015
Spinal cord (SC) atrophy, i.e. a reduction in the SC cross-sectional area (CSA) over time, can be... more Spinal cord (SC) atrophy, i.e. a reduction in the SC cross-sectional area (CSA) over time, can be measured by means of image segmentation using magnetic resonance imaging (MRI). However, segmentation methods have been limited by factors relating to reproducibility or sensitivity to change. The purpose of this study was to evaluate a fully automated SC segmentation method (PropSeg), and compare this to a semi-automated active surface (AS) method, in healthy controls (HC) and people with multiple sclerosis (MS). MRI data from 120 people were retrospectively analysed; 26 HC, 21 with clinically isolated syndrome, 26 relapsing remitting MS, 26 primary and 21 secondary progressive MS. MRI data from 40 people returning after one year were also analysed. CSA measurements were obtained within the cervical SC. Reproducibility of the measurements was assessed using the intraclass correlation coefficient (ICC). A comparison between mean CSA changes obtained with the two methods over time was performed using multivariate structural equation regression models. Associations between CSA measures and clinical scores were investigated using linear regression models. Compared to the AS method, the reproducibility of CSA measurements obtained with PropSeg was high, both in patients and in HC, with ICC > 0.98 in all cases. There was no significant difference between PropSeg and AS in terms of detecting change over time. Furthermore, PropSeg provided measures that correlated with physical disability, similar to the AS method. PropSeg is a time-efficient and reliable segmentation method, which requires no manual intervention, and may facilitate large multi-centre neuroprotective trials in progressive MS.
IEEE Transactions on Medical Imaging, 2015
Quantifying spinal cord (SC) atrophy in neurodegenerative and traumatic diseases brings important... more Quantifying spinal cord (SC) atrophy in neurodegenerative and traumatic diseases brings important diagnosis and prognosis information for the clinician. We recently developed the PropSeg method, which allows for fast, accurate and automatic segmentation of the SC on different types of MRI contrast (e.g., -, -and -weighted sequences) and any field of view. However, comparing measurements from the SC between subjects is hindered by the lack of a generic coordinate system for the SC. In this paper, we present a new framework combining PropSeg and a vertebral level identification method, thereby enabling direct inter-and intra-subject comparison of SC measurements for large cohort studies as well as for longitudinal studies. Our segmentation method is based on the multi-resolution propagation of tubular deformable models. Coupled with an automatic intervertebral disk identification method, our segmentation pipeline provides quantitative metrics of the SC and spinal canal such as cross-sectional areas and volumes in a generic coordinate system based on vertebral levels. This framework was validated on 17 healthy subjects and on one patient with SC injury against manual segmentation. Results have been compared with an existing active surface method and show high local and global accuracy for both SC and spinal canal (Dice coefficients =0.91 0.02) segmentation. Having a robust and automatic framework for SC segmentation and vertebral-based normalization opens the door to bias-free measurement of SC atrophy in large cohorts.
NeuroImage, 2014
The field of spinal cord MRI is lacking a common template, as existing for the brain, which would... more The field of spinal cord MRI is lacking a common template, as existing for the brain, which would allow extraction of multi-parametric data (diffusion-weighted, magnetization transfer, etc.) without user bias, thereby facilitating group analysis and multi-center studies. This paper describes a framework to produce an unbiased average anatomical template of the human spinal cord. The template was created by co-registering T2-weighted images (N = 16 healthy volunteers) using a series of pre-processing steps followed by non-linear registration. A white and gray matter probabilistic template was then merged to the average anatomical template, yielding the MNI-Poly-AMU template, which currently covers vertebral levels C1 to T6. New subjects can be registered to the template using a dedicated image processing pipeline. Validation was conducted on 16 additional subjects by comparing an automatic template-based segmentation and manual segmentation, yielding a median Dice coefficient of 0.89. The registration pipeline is rapid (~15 min), automatic after one C2/C3 landmark manual identification, and robust, thereby reducing subjective variability and bias associated with manual segmentation. The template can notably be used for measurements of spinal cord cross-sectional area, voxel-based morphometry, identification of anatomical features (e.g., vertebral levels, white and gray matter location) and unbiased extraction of multi-parametric data.
Medical Imaging 2014: Image Processing, 2014
ABSTRACT Spinal cord diseases or injuries can cause dysfunction of the sensory and locomotor syst... more ABSTRACT Spinal cord diseases or injuries can cause dysfunction of the sensory and locomotor systems. Segmentation of the spinal cord provides measures of atrophy and allows group analysis of multi-parametric MRI via inter-subject registration to a template. All these measures were shown to improve diagnostic and surgical intervention. We developed a framework to automatically segment the spinal cord on T2-weighted MR images, based on the propagation of a deformable model. The algorithm is divided into three parts: first, an initialization step detects the spinal cord position and orientation by using the elliptical Hough transform on multiple adjacent axial slices to produce an initial tubular mesh. Second, a low-resolution deformable model is iteratively propagated along the spinal cord. To deal with highly variable contrast levels between the spinal cord and the cerebrospinal fluid, the deformation is coupled with a contrast adaptation at each iteration. Third, a refinement process and a global deformation are applied on the low-resolution mesh to provide an accurate segmentation of the spinal cord. Our method was evaluated against a semi-automatic edge-based snake method implemented in ITK-SNAP (with heavy manual adjustment) by computing the 3D Dice coefficient, mean and maximum distance errors. Accuracy and robustness were assessed from 8 healthy subjects. Each subject had two volumes: one at the cervical and one at the thoracolumbar region. Results show a precision of 0.30 ± 0.05 mm (mean absolute distance error) in the cervical region and 0.27 ± 0.06 mm in the thoracolumbar region. The 3D Dice coefficient was of 0.93 for both regions.
International Journal of Optomechatronics, 2013
ABSTRACT This article introduces a novel structured light pattern designed to be compatible with ... more ABSTRACT This article introduces a novel structured light pattern designed to be compatible with the spatial light modulator (SLM) projection. The proposed pattern is a De Bruijn-based sequence applied to a combination of continuous and dashed lines for the pattern. The sequence is coded in the period and duty cycles of the dashed lines. It provides 16 different lines which limits to two the required number of dashed lines needed for identification. The segmentation has been made easier by alternating continuous and dashed lines. As required by the use of SLMs, the sequence has been adapted by making it symmetric. It has been improved by guaranteeing a hamming distance equal to two for two successive dashed lines. The implementation on a virtual model has shown that a subpixel accuracy has been achieved. This pattern has been developped for 3-D endoscopy.
2012 International Symposium on Optomechatronic Technologies (ISOT 2012), 2012
ABSTRACT This paper introduces a novel structured light pattern designed to be compatible with th... more ABSTRACT This paper introduces a novel structured light pattern designed to be compatible with the hologram projection. The proposed pattern is a De Bruijn-based sequence applied to a combination of continuous and dashed lines for the pattern. The sequence is coded in the period in the period and duty cycles of the dashed lines. It provides 16 different lines which limits to 2 the required number of lines needed for identification. The segmentation has been made easier by alternating continuous and dashed lines. As required by the use of holograms, the sequence has been adapted by making it symmetric. It has been improved by guaranteeing a hamming distance equal to two for two successive dashed lines. The implementation on a virtual model has shown that subpixel accuracy has been achieved. We developped this pattern for 3D endoscopy.
Neurosurgery, 2016
Diffusion tensor imaging (DTI), magnetization transfer (MT), and T2*-weighted imaging measure asp... more Diffusion tensor imaging (DTI), magnetization transfer (MT), and T2*-weighted imaging measure aspects of spinal cord microstructure. This study investigates if these techniques can quantify injury to individual white matter (WM) tracts and correlate with focal neurological impairments in degenerative cervical myelopathy (DCM). Fifty-seven DCM patients (age 56.7; 61% male; 32 mild, 16 moderate, 9 severe) underwent comprehensive clinical assessments and multimodal MRI (3T GE). Analysis with Spinal Cord Toolbox extracted fractional anisotropy (FA), MT ratio (MTR), and T2* WM/gray matter (GM) ratio (representing gray-white contrast) from regions of interest including: total WM, lateral corticospinal tracts (LCSTs), dorsal columns (DCs), and spinothalamic tracts (STTs) at C1-C2. Spearman correlations were calculated between total WM and global disability (mJOA), and between metrics in unilateral/bilateral WM tracts and measures of focal neurological impairment: mJOA upper/lower extremity...
GigaScience, 2016
Brainhack events offer a novel workshop format with participant-generated content that caters to ... more Brainhack events offer a novel workshop format with participant-generated content that caters to the rapidly growing open neuroscience community. Including components from hackathons and unconferences, as well as parallel educational sessions, Brainhack fosters novel collaborations around the interests of its attendees. Here we provide an overview of its structure, past events, and example projects. Additionally, we outline current innovations such as regional events and post-conference publications. Through introducing Brainhack to the wider neuroscience community, we hope to provide a unique conference format that promotes the features of collaborative, open science.
Magnetic Resonance Materials in Physics, Biology and Medicine, 2016
Segmenting the spinal cord contour is a necessary step for quantifying spinal cord atrophy in var... more Segmenting the spinal cord contour is a necessary step for quantifying spinal cord atrophy in various diseases. Delineating gray matter (GM) and white matter (WM) is also useful for quantifying GM atrophy or for extracting multiparametric MRI metrics into specific WM tracts. Spinal cord segmentation in clinical research is not as developed as brain segmentation, however with the substantial improvement of MR sequences adapted to spinal cord MR investigations, the field of spinal cord MR segmentation has advanced greatly within the last decade. Segmentation techniques with variable accuracy and degree of complexity have been developed and reported in the literature. In this paper, we review some of the existing methods for cord and WM/GM segmentation, including intensity-based, surface-based, and image-based methods. We also provide recommendations for validating spinal cord segmentation techniques, as it is important to understand the intrinsic characteristics of the methods and to evaluate their performance and limitations. Lastly, we illustrate some applications in the healthy and pathological spinal cord. One conclusion of this review is that robust and automatic segmentation is clinically relevant, as it would allow for longitudinal and group studies free from user bias as well as reproducible multicentric studies in large populations, thereby helping to further our understanding of the spinal cord pathophysiology and to develop new criteria for early detection of subclinical evolution for prognosis prediction and for patient management. Another conclusion is that at the present time, no single method adequately segments the cord and its substructure in all the cases encountered (abnormal intensities, loss of contrast, deformation of the cord, etc.). A combination of different approaches is thus advised for future developments, along with the introduction of probabilistic shape models. Maturation of standardized frameworks, multiplatform availability, inclusion in large suite and data sharing would also ultimately benefit to the community.
NeuroImage: Clinical, 2015
Spinal cord (SC) atrophy, i.e. a reduction in the SC cross-sectional area (CSA) over time, can be... more Spinal cord (SC) atrophy, i.e. a reduction in the SC cross-sectional area (CSA) over time, can be measured by means of image segmentation using magnetic resonance imaging (MRI). However, segmentation methods have been limited by factors relating to reproducibility or sensitivity to change. The purpose of this study was to evaluate a fully automated SC segmentation method (PropSeg), and compare this to a semi-automated active surface (AS) method, in healthy controls (HC) and people with multiple sclerosis (MS). MRI data from 120 people were retrospectively analysed; 26 HC, 21 with clinically isolated syndrome, 26 relapsing remitting MS, 26 primary and 21 secondary progressive MS. MRI data from 40 people returning after one year were also analysed. CSA measurements were obtained within the cervical SC. Reproducibility of the measurements was assessed using the intraclass correlation coefficient (ICC). A comparison between mean CSA changes obtained with the two methods over time was performed using multivariate structural equation regression models. Associations between CSA measures and clinical scores were investigated using linear regression models. Compared to the AS method, the reproducibility of CSA measurements obtained with PropSeg was high, both in patients and in HC, with ICC > 0.98 in all cases. There was no significant difference between PropSeg and AS in terms of detecting change over time. Furthermore, PropSeg provided measures that correlated with physical disability, similar to the AS method. PropSeg is a time-efficient and reliable segmentation method, which requires no manual intervention, and may facilitate large multi-centre neuroprotective trials in progressive MS.
IEEE Transactions on Medical Imaging, 2015
Quantifying spinal cord (SC) atrophy in neurodegenerative and traumatic diseases brings important... more Quantifying spinal cord (SC) atrophy in neurodegenerative and traumatic diseases brings important diagnosis and prognosis information for the clinician. We recently developed the PropSeg method, which allows for fast, accurate and automatic segmentation of the SC on different types of MRI contrast (e.g., -, -and -weighted sequences) and any field of view. However, comparing measurements from the SC between subjects is hindered by the lack of a generic coordinate system for the SC. In this paper, we present a new framework combining PropSeg and a vertebral level identification method, thereby enabling direct inter-and intra-subject comparison of SC measurements for large cohort studies as well as for longitudinal studies. Our segmentation method is based on the multi-resolution propagation of tubular deformable models. Coupled with an automatic intervertebral disk identification method, our segmentation pipeline provides quantitative metrics of the SC and spinal canal such as cross-sectional areas and volumes in a generic coordinate system based on vertebral levels. This framework was validated on 17 healthy subjects and on one patient with SC injury against manual segmentation. Results have been compared with an existing active surface method and show high local and global accuracy for both SC and spinal canal (Dice coefficients =0.91 0.02) segmentation. Having a robust and automatic framework for SC segmentation and vertebral-based normalization opens the door to bias-free measurement of SC atrophy in large cohorts.
NeuroImage, 2014
The field of spinal cord MRI is lacking a common template, as existing for the brain, which would... more The field of spinal cord MRI is lacking a common template, as existing for the brain, which would allow extraction of multi-parametric data (diffusion-weighted, magnetization transfer, etc.) without user bias, thereby facilitating group analysis and multi-center studies. This paper describes a framework to produce an unbiased average anatomical template of the human spinal cord. The template was created by co-registering T2-weighted images (N = 16 healthy volunteers) using a series of pre-processing steps followed by non-linear registration. A white and gray matter probabilistic template was then merged to the average anatomical template, yielding the MNI-Poly-AMU template, which currently covers vertebral levels C1 to T6. New subjects can be registered to the template using a dedicated image processing pipeline. Validation was conducted on 16 additional subjects by comparing an automatic template-based segmentation and manual segmentation, yielding a median Dice coefficient of 0.89. The registration pipeline is rapid (~15 min), automatic after one C2/C3 landmark manual identification, and robust, thereby reducing subjective variability and bias associated with manual segmentation. The template can notably be used for measurements of spinal cord cross-sectional area, voxel-based morphometry, identification of anatomical features (e.g., vertebral levels, white and gray matter location) and unbiased extraction of multi-parametric data.
Medical Imaging 2014: Image Processing, 2014
ABSTRACT Spinal cord diseases or injuries can cause dysfunction of the sensory and locomotor syst... more ABSTRACT Spinal cord diseases or injuries can cause dysfunction of the sensory and locomotor systems. Segmentation of the spinal cord provides measures of atrophy and allows group analysis of multi-parametric MRI via inter-subject registration to a template. All these measures were shown to improve diagnostic and surgical intervention. We developed a framework to automatically segment the spinal cord on T2-weighted MR images, based on the propagation of a deformable model. The algorithm is divided into three parts: first, an initialization step detects the spinal cord position and orientation by using the elliptical Hough transform on multiple adjacent axial slices to produce an initial tubular mesh. Second, a low-resolution deformable model is iteratively propagated along the spinal cord. To deal with highly variable contrast levels between the spinal cord and the cerebrospinal fluid, the deformation is coupled with a contrast adaptation at each iteration. Third, a refinement process and a global deformation are applied on the low-resolution mesh to provide an accurate segmentation of the spinal cord. Our method was evaluated against a semi-automatic edge-based snake method implemented in ITK-SNAP (with heavy manual adjustment) by computing the 3D Dice coefficient, mean and maximum distance errors. Accuracy and robustness were assessed from 8 healthy subjects. Each subject had two volumes: one at the cervical and one at the thoracolumbar region. Results show a precision of 0.30 ± 0.05 mm (mean absolute distance error) in the cervical region and 0.27 ± 0.06 mm in the thoracolumbar region. The 3D Dice coefficient was of 0.93 for both regions.
International Journal of Optomechatronics, 2013
ABSTRACT This article introduces a novel structured light pattern designed to be compatible with ... more ABSTRACT This article introduces a novel structured light pattern designed to be compatible with the spatial light modulator (SLM) projection. The proposed pattern is a De Bruijn-based sequence applied to a combination of continuous and dashed lines for the pattern. The sequence is coded in the period and duty cycles of the dashed lines. It provides 16 different lines which limits to two the required number of dashed lines needed for identification. The segmentation has been made easier by alternating continuous and dashed lines. As required by the use of SLMs, the sequence has been adapted by making it symmetric. It has been improved by guaranteeing a hamming distance equal to two for two successive dashed lines. The implementation on a virtual model has shown that a subpixel accuracy has been achieved. This pattern has been developped for 3-D endoscopy.
2012 International Symposium on Optomechatronic Technologies (ISOT 2012), 2012
ABSTRACT This paper introduces a novel structured light pattern designed to be compatible with th... more ABSTRACT This paper introduces a novel structured light pattern designed to be compatible with the hologram projection. The proposed pattern is a De Bruijn-based sequence applied to a combination of continuous and dashed lines for the pattern. The sequence is coded in the period in the period and duty cycles of the dashed lines. It provides 16 different lines which limits to 2 the required number of lines needed for identification. The segmentation has been made easier by alternating continuous and dashed lines. As required by the use of holograms, the sequence has been adapted by making it symmetric. It has been improved by guaranteeing a hamming distance equal to two for two successive dashed lines. The implementation on a virtual model has shown that subpixel accuracy has been achieved. We developped this pattern for 3D endoscopy.