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Iman Brouwer

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7 papers

2 author rows

YNICL Journal 2024 Journal Article

Scanner-specific optimisation of automated lesion segmentation in MS

David R. van Nederpelt
Giuseppe Pontillo
Mar Barrantes-Cepas
Iman Brouwer
Eva M.M. Strijbis
Menno M. Schoonheim
Bastiaan Moraal
Bas Jasperse

BACKGROUND & OBJECTIVE: Automatic lesion segmentation techniques on MRI scans of people with multiple sclerosis (pwMS) could support lesion detection and segmentation in trials and clinical practice. However, knowledge on their reliability across scanners is limited, hampering clinical implementation. The aim of this study was to investigate the within-scanner repeatability and between-scanner reproducibility of lesion segmentation tools in pwMS across three different scanners and examine their accuracy compared to manual segmentations with and without optimization. METHODS: 30 pwMS underwent a scan and rescan on three MRI scanners. GE Discovery MR750 (3.0 T), Siemens Sola (1.5 T) and Siemens Vida (3.0 T)). 3D-FLuid Attenuated Inversion Recovery (3D-FLAIR) and 3D T1-weighted scans were acquired on each scanner. Lesion segmentation involved preprocessing and automatic segmentation using the Lesion Segmentation Toolbox (LST) and nicMSlesions (nicMS) as well as manual segmentation. Both automated segmentation techniques were used with default settings, and with settings optimized to match manual segmentations for each scanner specifically and combined for the three scanners. LST settings were optimized by adjusting the threshold to improve the Dice similarity coefficient (DSC) for each scanner separately and a combined threshold for all scanners. For nicMS the last layers were retrained, once with the multi-scanner data to represent a combined optimization and once separately for each scanner for scanner specific optimization. Volumes and counts were extracted. DSC was calculated for accuracy, and reliability was assessed using intra-class correlation coefficients (ICC). Differences in DSC between software was tested with a repeated measures ANOVA and when appropriate post-hoc paired t-tests using Bonferroni correction. RESULTS: Scanner-specific optimization significantly improved DSC for LST compared to default and combined settings, except for the GE scanner. NicMS showed significantly higher DSC for both the scanner-specific and combined optimization than default. Within-scanner repeatability was excellent (ICC>0.9) for volume and counts. Between-scanner ICC for volume between Vida and Sola was higher (0.94-0.99) than between GE MR750 and Vida or Sola (0.18-0.93), with improved ICCs for nicMS scanner-specific (0.87-0.93) compared to others (0.18-0.79). This was not present for Sola vs. Vida where all ICCs were excellent (>0.94). CONCLUSION: Scanner-specific optimization strategies proved effective in mitigating inter-scanner variability, addressing the issue of insufficient reproducibility and accuracy found with default settings.

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YNICL Journal 2023 Journal Article

The spatio-temporal relationship between concurrent lesion and brain atrophy changes in early multiple sclerosis: A post-hoc analysis of the REFLEXION study

Giordano Gentile
Rozemarijn M. Mattiesing
Iman Brouwer
Ronald A. van Schijndel
Bernard M.J. Uitdehaag
Jos W.R. Twisk
Ludwig Kappos
Mark S. Freedman

BACKGROUND: White matter (WM) lesions and brain atrophy are present early in multiple sclerosis (MS). However, their spatio-temporal relationship remains unclear. METHODS: Yearly magnetic resonance images were analysed in 387 patients with a first clinical demyelinating event (FCDE) from the 5-year REFLEXION study. Patients received early (from baseline; N = 258; ET) or delayed treatment (from month-24; N = 129; DT) with subcutaneous interferon beta-1a. FSL-SIENA/VIENA were used to provide yearly percentage volume change of brain (PBVC) and ventricles (PVVC). Yearly total lesion volume change (TLVC) was determined by a semi-automated method. Using linear mixed models and voxel-wise analyses, we firstly investigated the overall relationship between TLVC and PBVC and between TLVC and PVVC in the same follow-up period. Analyses were then separately performed for: the untreated period of DT patients (first two years), the first year of treatment (year 1 for ET and year 3 for DT), and a period where patients had received at least 1 year of treatment (stable treatment; ET: years 2, 3, 4, and 5; DT: years 4 and 5). RESULTS: Whole brain: across the whole study period, lower TLVC was related to faster atrophy (PBVC: B = 0.046, SE = 0.013, p < 0.001; PVVC: B = -0.466, SE = 0.118, p < 0.001). Within the untreated period of DT patients, lower TLVC was related to faster atrophy (PBVC: B = 0.072, SE = 0.029, p = 0.013; PVVC: B = -0.917, SE = 0.306, p = 0.003). A similar relationship was found within the first year of treatment of ET patients (PBVC: B = 0.081, SE = 0.027, p = 0.003; PVVC: B = -1.08, SE = 0.284, p < 0.001), consistent with resolving oedema and pseudo-atrophy. Voxel-wise: overall, higher TLVC was related to faster ventricular enlargement. Lower TLVC was related to faster widespread atrophy in year 1 in both ET (first year of treatment) and DT (untreated) patients. In the second untreated year of DT patients and within the stable treatment period of ET patients (year 4), faster periventricular and occipital lobe atrophy was associated with higher TLVC. CONCLUSIONS: WM lesion changes and atrophy occurred simultaneously in early MS. Spatio-temporal correspondence of these two processes involved mostly the periventricular area. Within the first year of the study, in both treatment groups, faster atrophy was linked to lower lesion volume changes, consistent with higher shrinking and disappearing lesion activity. This might reflect the pseudo-atrophy phenomenon that is probably related to the therapy driven (only in ET patients, as they received treatment from baseline) and "natural" (both ET and DT patients entered the study after a FCDE) resolution of oedema. In an untreated period and later on during stable treatment, (real) atrophy was related to higher lesion volume changes, consistent with increased new and enlarging lesion activity.

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YNICL Journal 2022 Journal Article

The spatio-temporal relationship between white matter lesion volume changes and brain atrophy in clinically isolated syndrome and early multiple sclerosis

Rozemarijn M. Mattiesing
Giordano Gentile
Iman Brouwer
Ronald A. van Schijndel
Bernard M.J. Uitdehaag
Jos W.R. Twisk
Ludwig Kappos
Mark S. Freedman

BACKGROUND: White matter lesions and brain atrophy are both present early in multiple sclerosis. However, the spatio-temporal relationship between atrophy and lesion processes remains unclear. METHODS: Yearly magnetic resonance images were analyzed in 392 patients with clinically isolated syndrome from the 5-year REFLEX/REFLEXION studies. Patients received early treatment (from baseline; N = 262) or delayed treatment (from month-24; N = 130) with subcutaneous interferon beta-1a. Global and central atrophy were assessed using FSL-SIENA to provide yearly percentage volume change of brain and ventricles, respectively. Yearly total lesion volume change was calculated by subtracting the sum of the negative lesion volume change (disappearing + shrinking) from the positive lesion volume change (new + enlarging) for each yearly interval, as determined by an in-house developed semi-automated method. Using linear mixed models, during the period where patients had received ≥1 year of treatment, we investigated whether total lesion volume change was associated with percentage brain volume change or percentage ventricular volume change in the next year, and vice versa. RESULTS: Higher total lesion volume change was related to significantly faster global atrophy (percentage brain volume change) in the next year (B = - 0.113, SE = 0.022, p < 0.001). In patients receiving early treatment only, total lesion volume change was also associated with percentage ventricular volume change in the next year (B = 1.348, SE = 0.181, p < 0.001). Voxel-wise analyses showed that in patients receiving early treatment, higher total lesion volume change in years 2, 3, and 4 was related to faster atrophy in the next year, and in year 4 this relationship was stronger in patients receiving delayed treatment. Interestingly, faster atrophy was related to higher total lesion volume change in the next year (percentage brain volume change: B = - 0.136, SE = 0.062, p = 0.028; percentage ventricular volume change: B = 0.028, SE = 0.008, p < 0.001). CONCLUSIONS: Higher lesion volume changes were associated with faster atrophy in the next year. Interestingly, there was also an association between faster atrophy and higher lesion volume changes in the next year.

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YNICL Journal 2021 Journal Article

Manual and automated tissue segmentation confirm the impact of thalamus atrophy on cognition in multiple sclerosis: A multicenter study

Jessica Burggraaff
Yao Liu
Juan C. Prieto
Jorge Simoes
Alexandra de Sitter
Serena Ruggieri
Iman Brouwer
Birgit I. Lissenberg-Witte

BACKGROUND AND RATIONALE: Thalamus atrophy has been linked to cognitive decline in multiple sclerosis (MS) using various segmentation methods. We investigated the consistency of the association between thalamus volume and cognition in MS for two common automated segmentation approaches, as well as fully manual outlining. METHODS: Standardized neuropsychological assessment and 3-Tesla 3D-T1-weighted brain MRI were collected (multi-center) from 57 MS patients and 17 healthy controls. Thalamus segmentations were generated manually and using five automated methods. Agreement between the algorithms and manual outlines was assessed with Bland-Altman plots; linear regression assessed the presence of proportional bias. The effect of segmentation method on the separation of cognitively impaired (CI) and preserved (CP) patients was investigated through Generalized Estimating Equations; associations with cognitive measures were investigated using linear mixed models, for each method and vendor. RESULTS: In smaller thalami, automated methods systematically overestimated volumes compared to manual segmentations [ρ=(-0.42)-(-0.76); p-values < 0.001). All methods significantly distinguished CI from CP MS patients, except manual outlines of the left thalamus (p = 0.23). Poorer global neuropsychological test performance was significantly associated with smaller thalamus volumes bilaterally using all methods. Vendor significantly affected the findings. CONCLUSION: Automated and manual thalamus segmentation consistently demonstrated an association between thalamus atrophy and cognitive impairment in MS. However, a proportional bias in smaller thalami and choice of MRI acquisition system might impact the effect size of these findings.

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YNICL Journal 2021 Journal Article

The sequence of structural, functional and cognitive changes in multiple sclerosis

Iris Dekker
Menno M. Schoonheim
Vikram Venkatraghavan
Anand J.C. Eijlers
Iman Brouwer
Esther E. Bron
Stefan Klein
Mike P. Wattjes

BACKGROUND: As disease progression remains poorly understood in multiple sclerosis (MS), we aim to investigate the sequence in which different disease milestones occur using a novel data-driven approach. METHODS: We analysed a cohort of 295 relapse-onset MS patients and 96 healthy controls, and considered 28 features, capturing information on T2-lesion load, regional brain and spinal cord volumes, resting-state functional centrality ("hubness"), microstructural tissue integrity of major white matter (WM) tracts and performance on multiple cognitive tests. We used a discriminative event-based model to estimate the sequence of biomarker abnormality in MS progression in general, as well as specific models for worsening physical disability and cognitive impairment. RESULTS: We demonstrated that grey matter (GM) atrophy of the cerebellum, thalamus, and changes in corticospinal tracts are early events in MS pathology, whereas other WM tracts as well as the cognitive domains of working memory, attention, and executive function are consistently late events. The models for disability and cognition show early functional changes of the default-mode network and earlier changes in spinal cord volume compared to the general MS population. Overall, GM atrophy seems crucial due to its early involvement in the disease course, whereas WM tract integrity appears to be affected relatively late despite the early onset of WM lesions. CONCLUSION: Data-driven modelling revealed the relative occurrence of both imaging and non-imaging events as MS progresses, providing insights into disease propagation mechanisms, and allowing fine-grained staging of patients for monitoring purposes.

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YNICL Journal 2019 Journal Article

Novel imaging phantom for accurate and robust measurement of brain atrophy rates using clinical MRI

Houshang Amiri
Iman Brouwer
Joost P.A. Kuijer
Jan C. de Munck
Frederik Barkhof
Hugo Vrenken

Brain volume loss, or atrophy, has been proven to be an important characteristic of neurological diseases such as Alzheimer's disease and multiple sclerosis. To use atrophy rate as a reliable clinical biomarker and to increase statistical power in clinical treatment trials, measurement variability needs to be minimized. Among other sources, systematic differences between different MR scanners are suspected to contribute to this variability. In this study we developed and performed initial validation tests of an MR-compatible phantom and analysis software for robust and reliable evaluation of the brain volume loss. The phantom contained three inflatable models of brain structures, i.e. cerebral hemisphere, putamen, and caudate nucleus. Software to reliably quantify volumes form the phantom images was also developed. To validate the method, the phantom was imaged using 3D T1-weighted protocols at three clinical 3T MR scanners from different vendors. Calculated volume change from MRI was compared with the known applied volume change using ICC and mean absolute difference. As assessed by the ICC, the agreement between our developed software and the applied volume change for different structures ranged from 0.999-1 for hemisphere, 0.976-0.998 for putamen, and 0.985-0.999 for caudate nucleus. The mean absolute differences between measured and applied volume change were 109-332 μL for hemisphere, 2.9-11.9 μL for putamen, and 2.2-10.1 μL for caudate nucleus. This method offers a reliable and robust measurement of volume change using MR images and could potentially be used to standardize clinical measurement of atrophy rates.

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ICRA Conference 2004 Conference Paper

Simulating Cheap Hardware: a Platform for Evaluating Cost-performance Trade-offs in Haptic Hardware Design

Iman Brouwer
Karon E. MacLean
Antony J. Hodgson

This work describes a platform devised to explore the impact on task execution in a virtual environment of the quality, and therefore cost, of the system's haptic hardware. This platform is a complex haptic interface in which hardware quality can be varied in simulation. Software intercepts the position and force signals between the haptic hardware and the virtual environment software, and alters them to supply the effect of increased friction, cogging, backlash, inertia and/or lower force output. All parameters of the introduced effects can be set independently or in combination and on a continuous scale; a primary contribution is the creation of haptically realistic effect models that are stable in combination on complex hardware. This work is part of a larger project in which we test the effect of the simulated degradations on surgeons performance in simulated laparoscopic tasks.

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