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CNRS research engineer (IR2)
tel : +33 4 91 38 47 12
fax : +33 4 91 25 65 39
short CV : pdf (last update Feb 25th, 2013)
Key Words
- image segmentation
- image registration
- sulcal lines extraction
- applied mathematics


- Responsable du pôle informatique et pilote du processus informatique dans le cadre de la démarche qualité du laboratoire (obtention de la certification ISO 9001-NFX-50-900 en 2016)
- CSSI du laboratoire
- Correspondant COM du laboratoire
- Chargé de la gestion du parc informatique, des commandes de matériel informatique, de l’aide à l’installation et à la sécurisation des postes de travail et serveur de données.
- Webmaster du site web du laboratoire
- Chargé de l’administration et de la gestion d’un cluster de calcul (SGE, Linux)
- Enseignant vacataire dans le master TSI

Current Research Interest and projects

My research field is related to algorithmics, pattern recognition and image segmentation and registration for medical applications, in particular human brain data analysis. From 2006 to 2011, I was a research engineer in LSIS and has recently participated in the BrainMorph project, funded by the french ‘Agence nationale de la Recherche’, dedicated to the development and validation of surface-based brain morphometrics methods. I developed the software tools necessary to use these methods, mostly within the BrainVisa software platform, in C++ and python programming languages.
Since 2012, I am CNRS research engineer (IR2) in the CRMBM Lab, and work in the research field of the functional organization of brain networks, muscle and spinal cord segmentation.
  • Brain segmentation : Development of sulcal line extraction on human brain surface for parameterization of the cortical surface
  • Muscle segmentation : Development of fully automatic segmentation method of muscle MR images that aimed at discriminating the subcutaneous adipose tissue and the intramuscular adipose tissue
  • Spinal Cord segmentation : Creating multi-modal and probabilistic atlas of the spinal cord for automatic pipeline segmentation.



Journal Article

  • Benacchio, S., Doutres, O., Le Troter, A., Varoquaux, A., Wagnac, E., Callot, V., and Sgard, F. “Estimation Of The Ear Canal Displacement Field Due To In-Ear Device Insertion Using A Registration Method On A Human-Like Artificial Ear”. Hearing Research 365: 16-27. doi:10.1016/j.heares.2018.05.019.
    Résumé : Passive and active in-ear devices (IED) occluding the ear canal are commonly used to (i) protect people from high noise levels (earplugs), (ii) assist people suffering from hearing impairment (hearing aids) or (iii) help people in listening from their sound systems (earbuds). However, the usability and/or efficiency of IEDs can be greatly affected by several discomfort components (physical, acoustical and functional). The mechanical pressure exerted by the IED onto the ear canal walls is greatly suspected to affect the aforementioned comfort components. This physical characteristic is closely related to the displacement field induced by the IED insertion, which has to be known for a better understanding of perceived discomfort. Thus, this paper proposes to validate a method based on medical images to estimate the displacement field of the ear canal walls due to the insertion of an IED. The approach is validated on a human-like artificial ear with canal geometry deformed using two custom molded IEDs with controlled shapes. These geometries are obtained using computed tomography imaging and the displacement field is computed using a registration method. The errors due to the ear canal segmentation and to the registration steps are small enough to compute a relevant estimation of the expected displacement field. Results show that the amplitude of the displacement and its location into the ear canal can be evaluated with an accuracy of ± 0.2 mm and ± 0.4 mm respectively. Preliminary results on images with a degraded resolution indicate that the proposed approach used to assess the displacement field of the ear canal walls using computed tomography images could be applied on magnetic resonance images, which is a preferred method to image human subject ear canals for future investigations.
    Mots-clés : crmbm, Deformation, Displacement, Ear canal, Earbud, Earplug, Hearing aids, snc.

  • Fouré, Alexandre, Ogier, Augustin C., Le Troter, Arnaud, Vilmen, Christophe, Feiweier, Thorsten, Guye, Maxime, Gondin, Julien, Besson, Pierre, and Bendahan, David. “Diffusion Properties And 3D Architecture Of Human Lower Leg Muscles Assessed With Ultra-High-Field-Strength Diffusion-Tensor Mr Imaging And Tractography: Reproducibility And Sensitivity To Sex Difference And Intramuscular Variability”. Radiology 287, no. 2: 592-607. doi:10.1148/radiol.2017171330.
    Résumé : Purpose To demonstrate the reproducibility of the diffusion properties and three-dimensional structural organization measurements of the lower leg muscles by using diffusion-tensor imaging (DTI) assessed with ultra-high-field-strength (7.0-T) magnetic resonance (MR) imaging and tractography of skeletal muscle fibers. On the basis of robust statistical mapping analyses, this study also aimed at determining the sensitivity of the measurements to sex difference and intramuscular variability. Materials and Methods All examinations were performed with ethical review board approval; written informed consent was obtained from all volunteers. Reproducibility of diffusion tensor indexes assessment including eigenvalues, mean diffusivity, and fractional anisotropy (FA) as well as muscle volume and architecture (ie, fiber length and pennation angle) were characterized in lower leg muscles (n = 8). Intramuscular variability and sex differences were characterized in young healthy men and women (n = 10 in each group). Student t test, statistical parametric mapping, correlation coefficients (Spearman rho and Pearson product-moment) and coefficient of variation (CV) were used for statistical data analysis. Results High reproducibility of measurements (mean CV ± standard deviation, 4.6% ± 3.8) was determined in diffusion properties and architectural parameters. Significant sex differences were detected in FA (4.2% in women for the entire lower leg; P = .001) and muscle volume (21.7% in men for the entire lower leg; P = .008), whereas architecture parameters were almost identical across sex. Additional differences were found independently of sex in diffusion properties and architecture along several muscles of the lower leg. Conclusion The high-spatial-resolution DTI assessed with 7.0-T MR imaging allows a reproducible assessment of structural organization of superficial and deep muscles, giving indirect information on muscle function. ©RSNA, 2018 Online supplemental material is available for this article.
    Mots-clés : crmbm, msk.

  • Mchinda, Samira, Varma, Gopal, Prevost, Valentin H., Le Troter, Arnaud, Rapacchi, Stanislas, Guye, Maxime, Pelletier, Jean, et al. “Whole Brain Inhomogeneous Magnetization Transfer (Ihmt) Imaging: Sensitivity Enhancement Within A Steady-State Gradient Echo Sequence”. Magnetic Resonance In Medicine 79, no. 5: 2607-2619. doi:10.1002/mrm.26907.
    Résumé : PURPOSE: To implement, characterize, and optimize an interleaved inhomogeneous magnetization transfer (ihMT) gradient echo sequence allowing for whole-brain imaging within a clinically compatible scan time. THEORY AND METHODS: A general framework for ihMT modelling was developed based on the Provotorov theory of radiofrequency saturation, which accounts for the dipolar order underpinning the ihMT effect. Experimental studies and numerical simulations were performed to characterize and optimize the ihMT-gradient echo dependency with sequence timings, saturation power, and offset frequency. The protocol was optimized in terms of maximum signal intensity and the reproducibility assessed for a nominal resolution of 1.5 mm isotropic. All experiments were performed on healthy volunteers at 1.5T. RESULTS: An important mechanism driving signal optimization and leading to strong ihMT signal enhancement that relies on the dynamics of radiofrequency energy deposition has been identified. By taking advantage of the delay allowed for readout between ihMT pulse bursts, it was possible to boost the ihMT signal by almost 2-fold compared to previous implementation. Reproducibility of the optimal protocol was very good, with an intra-individual error < 2%. CONCLUSION: The proposed sensitivity-boosted and time-efficient steady-state ihMT-gradient echo sequence, implemented and optimized at 1.5T, allowed robust high-resolution 3D ihMT imaging of the whole brain within a clinically compatible scan time. Magn Reson Med 79:2607-2619, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
    Mots-clés : crmbm, dipolar order, dual frequency RF saturation, ihMT, inhomogeneous magnetization transfer, magnetization transfer model, myelin, Provotorov theory of radiofrequency saturation, snc.


Journal Article

  • Boutière, Clémence, Rey, Caroline, Zaaraoui, Wafaa, Le Troter, Arnaud, Rico, Audrey, Crespy, Lydie, Achard, Sophie, et al. “Improvement Of Spasticity Following Intermittent Theta Burst Stimulation In Multiple Sclerosis Is Associated With Modulation Of Resting-State Functional Connectivity Of The Primary Motor Cortices”. Multiple Sclerosis (Houndmills, Basingstoke, England) 23, no. 6: 855-863. doi:10.1177/1352458516661640.
    Résumé : BACKGROUND: Intermittent theta burst stimulation (iTBS) of the primary motor cortex improves transiently lower limbs spasticity in multiple sclerosis (MS). However, the cerebral mechanisms underlying this effect have never been investigated. OBJECTIVE: To assess whether modulation of spasticity induced by iTBS is underlined by functional reorganization of the primary motor cortices. METHODS: A total of 17 patients with MS suffering from lower limbs spasticity were randomized to receive real iTBS or sham iTBS during the first half of a 5-week indoor rehabilitation programme. Spasticity was assessed using the Modified Ashworth Scale and the Visual Analogue Scale at baseline, after the stimulation session and at the end of the rehabilitation programme. Resting-state functional magnetic resonance imaging (fMRI) was performed at the three time points, and brain functional networks topology was analysed using graph-theoretical approach. RESULTS: At the end of stimulation, improvement of spasticity was greater in real iTBS group than in sham iTBS group ( p = 0.026). iTBS had a significant effect on the balance of the connectivity degree between the stimulated and the homologous primary motor cortex ( p = 0.005). Changes in inter-hemispheric balance were correlated with improvement of spasticity (rho = 0.56, p = 0.015). CONCLUSION: This longitudinal resting-state fMRI study evidences that functional reorganization of the primary motor cortices may underlie the effect of iTBS on spasticity in MS.

  • Dupont, Sara M., De Leener, Benjamin, Taso, Manuel, Le Troter, Arnaud, Nadeau, Sylvie, Stikov, Nikola, Callot, Virginie, and Cohen-Adad, Julien. “Fully-Integrated Framework For The Segmentation And Registration Of The Spinal Cord White And Gray Matter”. Neuroimage 150: 358-372. doi:10.1016/j.neuroimage.2016.09.026.
    Résumé : The spinal cord white and gray matter can be affected by various pathologies such as multiple sclerosis, amyotrophic lateral sclerosis or trauma. Being able to precisely segment the white and gray matter could help with MR image analysis and hence be useful in further understanding these pathologies, and helping with diagnosis/prognosis and drug development. Up to date, white/gray matter segmentation has mostly been done manually, which is time consuming, induces a bias related to the rater and prevents large-scale multi-center studies. Recently, few methods have been proposed to automatically segment the spinal cord white and gray matter. However, no single method exists that combines the following criteria: (i) fully automatic, (ii) works on various MRI contrasts, (iii) robust towards pathology and (iv) freely available and open source. In this study we propose a multi-atlas based method for the segmentation of the spinal cord white and gray matter that addresses the previous limitations. Moreover, to study the spinal cord morphology, atlas-based approaches are increasingly used. These approaches rely on the registration of a spinal cord template to an MR image, however the registration usually doesn't take into account the spinal cord internal structure and thus lacks accuracy. In this study, we propose a new template registration framework that integrates the white and gray matter segmentation to account for the specific gray matter shape of each individual subject. Validation of segmentation was performed in 24 healthy subjects using T2*-weighted images, in 8 healthy subjects using diffusion weighted images (exhibiting inverted white-to-gray matter contrast compared to T2*-weighted), and in 5 patients with spinal cord injury. The template registration was validated in 24 subjects using T2*-weighted data. Results of automatic segmentation on T2*-weighted images was in close correspondence with the manual segmentation (Dice coefficient in the white/gray matter of 0.91/0.71 respectively). Similarly, good results were obtained in data with inverted contrast (diffusion-weighted image) and in patients. When compared to the classical template registration framework, the proposed framework that accounts for gray matter shape significantly improved the quality of the registration (comparing Dice coefficient in gray matter: p=9.5×10-6). While further validation is needed to show the benefits of the new registration framework in large cohorts and in a variety of patients, this study provides a fully-integrated tool for quantitative assessment of white/gray matter morphometry and template-based analysis. All the proposed methods are implemented in the Spinal Cord Toolbox (SCT), an open-source software for processing spinal cord multi-parametric MRI data.

  • Fatehi, Farzad, Salort-Campana, Emmanuelle, Le Troter, Arnaud, Lareau-Trudel, Emilie, Bydder, Mark, Fouré, Alexandre, Guye, Maxime, Bendahan, David, and Attarian, Shahram. “Long-Term Follow-Up Of Mri Changes In Thigh Muscles Of Patients With Facioscapulohumeral Dystrophy: A Quantitative Study”. Plos One 12, no. 8: e0183825. doi:10.1371/journal.pone.0183825.
    Résumé : Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common hereditary muscular disorders. Currently FSHD has no known effective treatment and detailed data on the natural history are lacking. Determination of the efficacy of a given therapeutic approach might be difficult in FSHD given the slow and highly variable disease progression. Magnetic resonance imaging (MRI) has been widely used to qualitatively and quantitatively evaluate in vivo the muscle alterations in various neuromuscular disorders. The main aim of the present study was to investigate longitudinally the time-dependent changes occurring in thigh muscles of FSHD patients using quantitative MRI and to assess the potential relationships with the clinical findings. Thirty-five FSHD1 patients (17 females) were enrolled. Clinical assessment tools including manual muscle testing using medical research council score (MRC), and motor function measure (MFM) were recorded each year for a period ranging from 1 to 2 years. For the MRI measurements, we used a new quantitative index, i.e., the mean pixel intensity (MPI) calculated from the pixel-intensity distribution in T1 weighted images. The corresponding MPI scores were calculated for each thigh, for each compartment and for both thighs totally (MPItotal). The total mean pixel intensity (MPItotal) refers to the sum of each pixel signal intensity divided by the corresponding number of pixels. An increased MPItotal indicates both a raised fat infiltration together with a reduced muscle volume thereby illustrating disease progression. Clinical scores did not change significantly over time whereas MPItotal increased significantly from an initial averaged value of 39.6 to 41.1 with a corresponding rate of 0.62/year. While clinical scores and MPItotal measured at the start of the study were significantly related, no correlation was found between the rate of MPItotal and MRC sum score changes, MFMtotal and MFM subscores. The relative rate of MPItotal change was 2.3% (0.5-4.3)/year and was significantly higher than the corresponding rates measured for MRCS 0% (0-1.7) /year and MFMtotal 0% (0-2.0) /year (p = 0.000). On the basis of these results, we suggested that muscle MRI and more particularly the MPItotal index could be used as a reliable biomarker and outcome measure of disease progression. In slowly progressive myopathies such as FSHD, the MPItotal index might reveal subclinical changes, which could not be evidenced using clinical scales over a short period of time.
    Mots-clés : crmbm, Humans, Magnetic Resonance Imaging, msk, Muscle, Skeletal, Muscular Dystrophy, Facioscapulohumeral.

  • Leporq, Benjamin, Troter, Arnaud Le, Fur, Yann Le, Salort-Campana, Emmanuelle, Guye, Maxime, Beuf, Olivier, Attarian, Shahram, and Bendahan, David. “Combined Quantification Of Fatty Infiltration, T1-Relaxation Times And T2*-Relaxation Times In Normal-Appearing Skeletal Muscle Of Controls And Dystrophic Patients”. Magnetic Resonance Materials In Physics, Biology And Medicine 30, no. 4: 407-415. doi:10.1007/s10334-017-0616-1.
    Résumé : ObjectivesTo evaluate the combination of a fat–water separation method with an automated segmentation algorithm to quantify the intermuscular fatty-infiltrated fraction, the relaxation times, and the microscopic fatty infiltration in the normal-appearing muscle.Materials and methodsMR acquisitions were performed at 1.5T in seven patients with facio-scapulo-humeral dystrophy and eight controls. Disease severity was assessed using commonly used scales for the upper and lower limbs. The fat–water separation method provided proton density fat fraction (PDFF) and relaxation times maps (T2* and T1). The segmentation algorithm distinguished adipose tissue and normal-appearing muscle from the T2* map and combined active contours, a clustering analysis, and a morphological closing process to calculate the index of fatty infiltration (IFI) in the muscle compartment defined as the relative amount of pixels with the ratio between the number of pixels within IMAT and the total number of pixels (IMAT + normal appearing muscle).ResultsIn patients, relaxation times were longer and a larger fatty infiltration has been quantified in the normal-appearing muscle. T2* and PDFF distributions were broader. The relaxation times were correlated to the Vignos scale whereas the microscopic fatty infiltration was linked to the Medwin-Gardner-Walton scale. The IFI was linked to a composite clinical severity scale gathering the whole set of scales.ConclusionThe MRI indices quantified within the normal-appearing muscle could be considered as potential biomarkers of dystrophies and quantitatively illustrate tissue alterations such as inflammation and fatty infiltration.
    Mots-clés : crmbm, Magnetic Resonance Imaging, msk, Muscle dystrophies, Segmentation.

  • Ogier, Augustin, Sdika, Michael, Foure, Alexandre, Le Troter, Arnaud, and Bendahan, David. “Individual Muscle Segmentation In Mr Images: A 3D Propagation Through 2D Non-Linear Registration Approaches”. Conference Proceedings: .. Annual International Conference Of The Ieee Engineering In Medicine And Biology Society. Ieee Engineering In Medicine And Biology Society. Annual Conference 2017: 317-320. doi:10.1109/EMBC.2017.8036826.
    Résumé : Manual and automated segmentation of individual muscles in magnetic resonance images have been recognized as challenging given the high variability of shapes between muscles and subjects and the discontinuity or lack of visible boundaries between muscles. In the present study, we proposed an original algorithm allowing a semi-automatic transversal propagation of manually-drawn masks. Our strategy was based on several ascending and descending non-linear registration approaches which is similar to the estimation of a Lagrangian trajectory applied to manual masks. Using several manually-segmented slices, we have evaluated our algorithm on the four muscles of the quadriceps femoris group. We mainly showed that our 3D propagated segmentation was very accurate with an averaged Dice similarity coefficient value higher than 0.91 for the minimal manual input of only two manually-segmented slices.
    Mots-clés : crmbm, msk.

  • Wybrecht, D., Reuter, F., Pariollaud, F., Zaaraoui, W., Le Troter, A., Rico, A., Confort-Gouny, S., et al. “New Brain Lesions With No Impact On Physical Disability Can Impact Cognition In Early Multiple Sclerosis: A Ten-Year Longitudinal Study”. Plos One 12, no. 11: e0184650. doi:10.1371/journal.pone.0184650.
    Résumé : OBJECTIVE: In early multiple sclerosis, although brain T2 lesions accrual are hallmark of the disease, only weak correlations were found between T2 lesions accrual and EDSS progression, the disability scale commonly used in multiple sclerosis studies. This may be related to the very poor sensitivity of EDSS to cognitive dysfunctions that may occur and progress from the first stage of the disease. In the present study, we aimed to demonstrate that cognitive deficits progress during the first ten years of MS and are significantly impacted by new T2 lesions. METHODS: EDSS and extensive neuropsychological battery (22 measures) exploring memory, attention/speed of information processing and executive functions were assessed at baseline, Year 1 and Year 10 in 26 patients enrolled after their first clinical attack. To limit the bias of test-retest effect, only measures obtained at Year 1 and Year 10 were reported in the analysis. Raw scores of patients were transformed into z-scores using published normative data when available or scores of matched controls. Lesion probability mapping was used to assess the potential relationships between T2 lesions accumulation, cognitive decline and EDSS progression (P<0.05, FWE-corrected). RESULTS: At Year 1, 27% of patients showed attention/speed of information processing deficits, 11.5% executive dysfunction and 11.5% memory impairment. During the follow-up, frequency and severity of executive dysfunction increased (from 11.5% of patients at Year 1 to 42% at Year 10, p<0.01) while no significant changes were evidenced for the other cognitive domains. Median EDSS increased from 0.5 [range: 0-3] at Year 1 to 2.5 [range: 0-6.5] at Year 10 (p<0.001). During the ten-year follow-up, lesions accumulation in the left cerebellum and semi-ovale centers was associated with EDSS progression. In contrast, most lesions accumulation in the frontal, parietal and temporal lobes were associated with cognitive decline but had no effect on EDSS progression. CONCLUSION: The present study provides strong evidence that clinically silent T2 lesions impact cognition in early MS. In daily practice, early prevention of T2 lesions accrual may be useful to limit cognitive decline.
    Mots-clés : crmbm, snc.


Journal Article

  • Donadieu, Maxime, Le Fur, Yann, Confort-Gouny, Sylviane, Le Troter, Arnaud, Guye, Maxime, and Ranjeva, Jean-Philippe. “Evidencing Different Neurochemical Profiles Between Thalamic Nuclei Using High Resolution 2D-Press Semi-Laser (1)H-Mrsi At 7 T”. Magma (New York, N.y.) 29, no. 3: 491-501. doi:10.1007/s10334-016-0556-1.
    Résumé : OBJECTIVE: To demonstrate that high resolution (1)H semi-LASER MRSI acquired at 7 T permits discrimination of metabolic patterns of different thalamic nuclei. MATERIALS AND METHODS: Thirteen right-handed healthy volunteers were explored at 7 T using a high-resolution 2D-semi-LASER (1)H-MRSI sequence to determine the relative levels of N-Acetyl Aspartate (NAA), choline (Cho) and creatine-phosphocreatine (Cr) in eight VOIs (volume <0.3 ml) centered on four different thalamic nuclei located on the Oxford thalamic connectivity atlas. Post-processing was done using the CSIAPO software. Chemical shift displacement of metabolites was evaluated on a phantom and correction factors were applied to in vivo data. RESULTS: The global assessment (ANOVA p < 0.05) of the neurochemical profiles (NAA, Cho and Cr levels) with thalamic nuclei and hemispheres as factors showed a significant global effect (F = 11.98, p < 0.0001), with significant effect of nucleus type (p < 0.0001) and hemisphere (p < 0.0001). Post hoc analyses showed differences in neurochemical profiles between the left and the right hemisphere (p < 0.05), and differences in neurochemical profiles between nuclei within each hemisphere (p < 0.05). CONCLUSION: For the first time, using high resolution 2D-PRESS semi-LASER (1)H-MRSI acquired at 7 T, we demonstrated that the neurochemical profiles were different between thalamic nuclei, and that these profiles were dependent on the brain hemisphere.
    Mots-clés : 1H-MRSI, Adult, Analysis of Variance, Aspartic Acid, Brain, Choline, Connectivity atlas, Creatine, crmbm, Female, Healthy Volunteers, Humans, Lasers, Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy, Male, Neurochemical profiles, Neurodegenerative Diseases, Phantoms, Imaging, Phosphocreatine, snc, Software, Spectrophotometry, Thalamic nuclei, Thalamus, Ultra high field, Young Adult.

  • Faivre, Anthony, Robinet, Emmanuelle, Guye, Maxime, Rousseau, Celia, Maarouf, Adil, Le Troter, Arnaud, Zaaraoui, Wafaa, et al. “Depletion Of Brain Functional Connectivity Enhancement Leads To Disability Progression In Multiple Sclerosis: A Longitudinal Resting-State Fmri Study”. Multiple Sclerosis (Houndmills, Basingstoke, England) 22, no. 13: 1695-1708. doi:10.1177/1352458516628657.
    Résumé : BACKGROUND: The compensatory effect of brain functional connectivity enhancement in relapsing-remitting multiple sclerosis (RRMS) remains controversial. OBJECTIVE: To characterize the relationships between brain functional connectivity changes and disability progression in RRMS. METHODS: Long-range connectivity, short-range connectivity, and density of connections were assessed using graph theoretical analysis of resting-state functional magnetic resonance imaging (fMRI) data acquired in 38 RRMS patients (disease duration: 120 ± 32 months) and 24 controls. All subjects were explored at baseline and all patients and six controls 2 years later. RESULTS: At baseline, levels of long-range and short-range brain functional connectivity were higher in patients compared to controls. During the follow-up, decrease in connections' density was inversely correlated with disability progression. Post-hoc analysis evidenced differential evolution of brain functional connectivity metrics in patients according to their level of disability at baseline: while patients with lowest disability at baseline experienced an increase in all connectivity metrics during the follow-up, patients with higher disability at baseline showed a decrease in the connectivity metrics. In these patients, decrease in the connectivity metrics was associated with disability progression. CONCLUSION: The study provides two main findings: (1) brain functional connectivity enhancement decreases during the disease course after reaching a maximal level, and (2) decrease in brain functional connectivity enhancement participates in disability progression.

  • Fatehi, F., Salort-Campana, E., Le Troter, A., Bendahan, D., and Attarian, S. “Muscle Mri Of Facioscapulohumeral Dystrophy (Fshd): A Growing Demand And A Promising Approach”. Revue Neurologique 172, no. 10: 566-571. doi:10.1016/j.neurol.2016.08.002.
    Résumé : Facioscapulohumeral muscular dystrophy (FSHD), an inherited and progressive muscle disorder, is among the most common hereditary muscle disorders. From a clinical vantage point, FSHD is characterized by weakness of the facial, shoulder (often with scapular winging), arm (including biceps and triceps) and abdominal muscles. Forearm muscles are usually spared and weakness is usually asymmetrical. Over the past few decades, muscle magnetic resonance imaging (MRI) has become established as a reliable and accurate noninvasive tool for the diagnosis and assessment of progression in neuromuscular diseases, showing specific patterns of muscle involvement for a number of myopathies. More recently, MRI has been used to noninvasively identify quantitative biomarkers, allowing evaluation of the natural progression of disease and assessment of therapeutic interventions. In the present review, the intention was to present the most significant MRI developments related to diagnosis and pattern recognition in FSHD and to discuss its capacity to provide outcome measures.
    Mots-clés : crmbm, Facioscapulohumeral dystrophy, FSHD, Measurement, MRI, msk, Pattern recognition.

  • Le Troter, Arnaud, Fouré, Alexandre, Guye, Maxime, Confort-Gouny, Sylviane, Mattei, Jean-Pierre, Gondin, Julien, Salort-Campana, Emmanuelle, and Bendahan, David. “Volume Measurements Of Individual Muscles In Human Quadriceps Femoris Using Atlas-Based Segmentation Approaches”. Magma (New York, N.y.) 29, no. 2: 245-257. doi:10.1007/s10334-016-0535-6.
    Résumé : OBJECTIVES: Atlas-based segmentation is a powerful method for automatic structural segmentation of several sub-structures in many organs. However, such an approach has been very scarcely used in the context of muscle segmentation, and so far no study has assessed such a method for the automatic delineation of individual muscles of the quadriceps femoris (QF). In the present study, we have evaluated a fully automated multi-atlas method and a semi-automated single-atlas method for the segmentation and volume quantification of the four muscles of the QF and for the QF as a whole. SUBJECTS AND METHODS: The study was conducted in 32 young healthy males, using high-resolution magnetic resonance images (MRI) of the thigh. The multi-atlas-based segmentation method was conducted in 25 subjects. Different non-linear registration approaches based on free-form deformable (FFD) and symmetric diffeomorphic normalization algorithms (SyN) were assessed. Optimal parameters of two fusion methods, i.e., STAPLE and STEPS, were determined on the basis of the highest Dice similarity index (DSI) considering manual segmentation (MSeg) as the ground truth. Validation and reproducibility of this pipeline were determined using another MRI dataset recorded in seven healthy male subjects on the basis of additional metrics such as the muscle volume similarity values, intraclass coefficient, and coefficient of variation. Both non-linear registration methods (FFD and SyN) were also evaluated as part of a single-atlas strategy in order to assess longitudinal muscle volume measurements. The multi- and the single-atlas approaches were compared for the segmentation and the volume quantification of the four muscles of the QF and for the QF as a whole. RESULTS: Considering each muscle of the QF, the DSI of the multi-atlas-based approach was high 0.87 ± 0.11 and the best results were obtained with the combination of two deformation fields resulting from the SyN registration method and the STEPS fusion algorithm. The optimal variables for FFD and SyN registration methods were four templates and a kernel standard deviation ranging between 5 and 8. The segmentation process using a single-atlas-based method was more robust with DSI values higher than 0.9. From the vantage of muscle volume measurements, the multi-atlas-based strategy provided acceptable results regarding the QF muscle as a whole but highly variable results regarding individual muscle. On the contrary, the performance of the single-atlas-based pipeline for individual muscles was highly comparable to the MSeg, thereby indicating that this method would be adequate for longitudinal tracking of muscle volume changes in healthy subjects. CONCLUSION: In the present study, we demonstrated that both multi-atlas and single-atlas approaches were relevant for the segmentation of individual muscles of the QF in healthy subjects. Considering muscle volume measurements, the single-atlas method provided promising perspectives regarding longitudinal quantification of individual muscle volumes.
    Mots-clés : crmbm, Fusion, Individual muscle volume measurements, MRI, msk, Multi-atlas-based segmentation, Non-linear registration, Quadriceps femoris muscle.

  • Ridley, Ben, Beltramone, Marion, Wirsich, Jonathan, Le Troter, Arnaud, Tramoni, Eve, Aubert, Sandrine, Achard, Sophie, Ranjeva, Jean-Philippe, Guye, Maxime, and Felician, Olivier. “Alien Hand, Restless Brain: Salience Network And Interhemispheric Connectivity Disruption Parallel Emergence And Extinction Of Diagonistic Dyspraxia”. Frontiers In Human Neuroscience 10: 307. doi:10.3389/fnhum.2016.00307.
    Résumé : Diagonistic dyspraxia (DD) is by far the most spectacular manifestation reported by sufferers of acute corpus callosum (CC) injury (so-called "split-brain"). In this form of alien hand syndrome, one hand acts at cross purposes with the other "against the patient's will". Although recent models view DD as a disorder of motor control, there is still little information regarding its neural underpinnings, due to widespread connectivity changes produced by CC insult, and the obstacle that non-volitional movements represent for task-based functional neuroimaging studies. Here, we studied patient AM, the first report of DD in patient with complete developmental CC agenesis. This unique case also offers the opportunity to study the resting-state connectomics of DD in the absence of diffuse changes subsequent to CC injury or surgery. AM developed DD following status epilepticus (SE) which resolved over a 2-year period. Whole brain functional connectivity (FC) was compared (Crawford-Howell [CH]) to 16 controls during the period of acute DD symptoms (Time 1) and after remission (Time 2). Whole brain graph theoretical models were also constructed and topological efficiency examined. At Time 1, disrupted FC was observed in inter-hemispheric and intra-hemispheric right edges, involving frontal superior and midline structures. Graph analysis indicated disruption of the efficiency of salience and right frontoparietal (FP) networks. At Time 2, after remission of diagnostic dyspraxia symptoms, FC and salience network changes had resolved. In sum, longitudinal analysis of connectivity in AM indicates that DD behaviors could result from disruption of systems that support the experience and control of volitional movements and the ability to generate appropriate behavioral responses to salient stimuli. This also raises the possibility that changes to large-scale functional architecture revealed by resting-state functional magnetic resonance imaging (fMRI) (rs-fMRI) may provide relevant information on the evolution of behavioral syndromes in addition to that provided by structural and task-based functional imaging.
    Mots-clés : alien hand, callosal agenesis, crmbm, disconnection syndrome, Epilepsy, Functional connectivity, graph theory, resting-state, snc.

  • Taso, Manuel, Girard, Olivier M., Duhamel, Guillaume, Le Troter, Arnaud, Feiweier, Thorsten, Guye, Maxime, Ranjeva, Jean-Philippe, and Callot, Virginie. “Tract-Specific And Age-Related Variations Of The Spinal Cord Microstructure: A Multi-Parametric Mri Study Using Diffusion Tensor Imaging (Dti) And Inhomogeneous Magnetization Transfer (Ihmt)”. Nmr In Biomedicine 29, no. 6: 817-832. doi:10.1002/nbm.3530.
    Résumé : Being able to finely characterize the spinal cord (SC) microstructure and its alterations is a key point when investigating neural damage mechanisms encountered in different central nervous system (CNS) pathologies, such as multiple sclerosis, amyotrophic lateral sclerosis or myelopathy. Based on novel methods, including inhomogeneous magnetization transfer (ihMT) and dedicated SC probabilistic atlas post-processing, the present study focuses on the in vivo characterization of the healthy SC tissue in terms of regional microstructure differences between (i) upper and lower cervical vertebral levels and (ii) sensory and motor tracts, as well as differences attributed to normal aging. Forty-eight healthy volunteers aged from 20 to 70 years old were included in the study and scanned at 3 T using axial high-resolution T2 *-w imaging, diffusion tensor imaging (DTI) and ihMT, at two vertebral levels (C2 and C5). A processing pipeline with minimal user intervention, SC segmentation and spatial normalization into a reference space was implemented in order to assess quantitative morphological and structural parameters (cross-sectional areas, scalar DTI and MT/ihMT metrics) in specific white and gray matter regions of interest. The multi-parametric MRI metrics collected allowed upper and lower cervical levels to be distinguished, with higher ihMT ratio (ihMTR), higher axial diffusivity (λ∥ ) and lower radial diffusivity (λ⊥ ) at C2 compared with C5. Significant differences were also observed between white matter fascicles, with higher ihMTR and lower λ∥ in motor tracts compared with posterior sensory tracts. Finally, aging was found to be associated with significant metric alterations (decreased ihMTR and λ∥ ). The methodology proposed here, which can be easily transferred to the clinic, provides new insights for SC characterization. It bears great potential to study focal and diffuse SC damage in neurodegenerative and demyelinating diseases. Copyright © 2016 John Wiley & Sons, Ltd.
    Mots-clés : aging, crmbm, diffusion tensor imaging (DTI), ihMT, inhomogeneous magnetization transfer (ihMT), microstructure, Multi-parametric MRI, snc, Spinal cord.


Journal Article

  • Fouré, Alexandre, Duhamel, Guillaume, Wegrzyk, Jennifer, Boudinet, Hélène, Mattei, Jean-Pierre, Le Troter, Arnaud, Bendahan, David, and Gondin, Julien. “Heterogeneity Of Muscle Damage Induced By Electrostimulation: A Multimodal Mri Study”. Medicine And Science In Sports And Exercise 47, no. 1: 166-175. doi:10.1249/MSS.0000000000000397.
    Résumé : PURPOSE: Neuromuscular electrostimulation (NMES) leads to a spatially fixed, synchronous, and superficial motor unit recruitment, which could induce muscle damage. Therefore, the extent of muscle damage and its spatial occurrence were expected to be heterogeneous across and along the quadriceps femoris (QF) muscles. The aim of the present study was to characterize muscle spatial heterogeneity in QF damage after a single bout of isometric NMES using multimodal magnetic resonance imaging (MRI). METHODS: Twenty-five young healthy males participated in this study. MRI investigations consisted of the assessment of muscle volume, transverse relaxation time (T2), and diffusion tensor imaging (DTI) in muscles positioned near the stimulation electrodes (i.e., vastus lateralis (VL) and vastus medialis (VM)) and muscles located outside the stimulated regions (i.e., vastus intermedius and rectus femoris). These measurements were performed 6 d before, and 2 d and 4 d (D4) after the NMES session. RESULTS: For the muscles placed in direct contact with the stimulation electrodes, volume (VL, +8.5%; VM, +3.8%), T2 (VL, +19.5%; VM, +6.7%) and radial diffusivity (λ3) (VL, + 7.3%; VM, +3.7%) significantly increased at D4. Whereas MRI parameter changes were larger for VL as compared with those for other QF muscles at D4, homogeneous alterations were found along all QF muscles. CONCLUSIONS: Isometric NMES induced specific and localized alterations in VL and VM, with heterogeneous damage amplitude among them. Potential effects of unaccustomed intermuscle shear stress during electrically evoked isometric contractions could be a key factor in the spatial occurrence and the extent of damage among QF muscles (especially in VL). The kinetics and extent of MRI changes varied between T2 and diffusion tensor imaging metrics, suggesting the involvement of different physiological processes.
    Mots-clés : crmbm, msk.

  • Fouré, Alexandre, Le Troter, Arnaud, Guye, Maxime, Mattei, Jean-Pierre, Bendahan, David, and Gondin, Julien. “Localization And Quantification Of Intramuscular Damage Using Statistical Parametric Mapping And Skeletal Muscle Parcellation”. Scientific Reports 5: 18580. doi:10.1038/srep18580.
    Résumé : In the present study, we proposed an original and robust methodology which combines the spatial normalization of skeletal muscle images, the statistical parametric mapping (SPM) analysis and the use of a specific parcellation in order to accurately localize and quantify the extent of skeletal muscle damage within the four heads of the quadriceps femoris. T2 maps of thigh muscles were characterized before, two (D2) and four (D4) days after 40 maximal isometric electrically-evoked contractions in 25 healthy young males. On the basis of SPM analysis of coregistrated T2 maps, the alterations were similarly detected at D2 and D4 in the superficial and distal regions of the vastus medialis (VM) whereas the proportion of altered muscle was higher in deep muscle regions of the vastus lateralis at D4 (deep: 35 ± 25%, superficial: 23 ± 15%) as compared to D2 (deep: 18 ± 13%, superficial: 17 ± 13%). The present methodology used for the first time on skeletal muscle would be of utmost interest to detect subtle intramuscular alterations not only for the diagnosis of muscular diseases but also for assessing the efficacy of potential therapeutic interventions and clinical treatment strategies.
    Mots-clés : crmbm, msk.

  • Lareau-Trudel, Emilie, Le Troter, Arnaud, Ghattas, Badih, Pouget, Jean, Attarian, Shahram, Bendahan, David, and Salort-Campana, Emmanuelle. “Muscle Quantitative Mr Imaging And Clustering Analysis In Patients With Facioscapulohumeral Muscular Dystrophy Type 1”. Plos One 10, no. 7: e0132717. doi:10.1371/journal.pone.0132717.
    Résumé : BACKGROUND: Facioscapulohumeral muscular dystrophy type 1 (FSHD1) is the third most common inherited muscular dystrophy. Considering the highly variable clinical expression and the slow disease progression, sensitive outcome measures would be of interest. METHODS AND FINDINGS: Using muscle MRI, we assessed muscular fatty infiltration in the lower limbs of 35 FSHD1 patients and 22 healthy volunteers by two methods: a quantitative imaging (qMRI) combined with a dedicated automated segmentation method performed on both thighs and a standard T1-weighted four-point visual scale (visual score) on thighs and legs. Each patient had a clinical evaluation including manual muscular testing, Clinical Severity Score (CSS) scale and MFM scale. The intramuscular fat fraction measured using qMRI in the thighs was significantly higher in patients (21.9 ± 20.4%) than in volunteers (3.6 ± 2.8%) (p<0.001). In patients, the intramuscular fat fraction was significantly correlated with the muscular fatty infiltration in the thighs evaluated by the mean visual score (p<0.001). However, we observed a ceiling effect of the visual score for patients with a severe fatty infiltration clearly indicating the larger accuracy of the qMRI approach. Mean intramuscular fat fraction was significantly correlated with CSS scale (p ≤ 0.01) and was inversely correlated with MMT score, MFM subscore D1 (p ≤ 0.01) further illustrating the sensitivity of the qMRI approach. Overall, a clustering analysis disclosed three different imaging patterns of muscle involvement for the thighs and the legs which could be related to different stages of the disease and put forth muscles which could be of interest for a subtle investigation of the disease progression and/or the efficiency of any therapeutic strategy. CONCLUSION: The qMRI provides a sensitive measurement of fat fraction which should also be of high interest to assess disease progression and any therapeutic strategy in FSHD1 patients.
    Mots-clés : Adipose Tissue, Adult, Case-Control Studies, Cluster Analysis, crmbm, Disease Progression, Female, Humans, Leg, Magnetic Resonance Imaging, Male, Middle Aged, msk, Muscle, Skeletal, Muscular Dystrophy, Facioscapulohumeral, Severity of Illness Index, Thigh.

  • Lecocq, Angèle, Le Fur, Yann, Maudsley, Andrew A., Le Troter, Arnaud, Sheriff, Sulaiman, Sabati, Mohamad, Donadieu, Maxime, et al. “Whole-Brain Quantitative Mapping Of Metabolites Using Short Echo Three-Dimensional Proton Mrsi”. Journal Of Magnetic Resonance Imaging: Jmri 42, no. 2: 280-289. doi:10.1002/jmri.24809.
    Résumé : BACKGROUND: To improve the extent over which whole brain quantitative three-dimensional (3D) magnetic resonance spectroscopic imaging (MRSI) maps can be obtained and be used to explore brain metabolism in a population of healthy volunteers. METHODS: Two short echo time (20 ms) acquisitions of 3D echo planar spectroscopic imaging at two orientations, one in the anterior commissure-posterior commissure (AC-PC) plane and the second tilted in the AC-PC +15° plane were obtained at 3 Tesla in a group of 10 healthy volunteers. B1 (+) , B1 (-) , and B0 correction procedures and normalization of metabolite signals with quantitative water proton density measurements were performed. A combination of the two spatially normalized 3D-MRSI, using a weighted mean based on the pixel wise standard deviation metabolic maps of each orientation obtained from the whole group, provided metabolite maps for each subject allowing regional metabolic profiles of all parcels of the automated anatomical labeling (AAL) atlas to be obtained. RESULTS: The combined metabolite maps derived from the two acquisitions reduced the regional intersubject variance. The numbers of AAL regions showing N-acetyl aspartate (NAA) SD/Mean ratios lower than 30% increased from 17 in the AC-PC orientation and 41 in the AC-PC+15° orientation, to a value of 76 regions of 116 for the combined NAA maps. Quantitatively, regional differences in absolute metabolite concentrations (mM) over the whole brain were depicted such as in the GM of frontal lobes (cNAA  = 10.03 + 1.71; cCho  = 1.78 ± 0.55; cCr  = 7.29 ± 1.69; cmIns  = 5.30 ± 2.67) and in cerebellum (cNAA  = 5.28 ± 1.77; cCho  = 1.60 ± 0.41; cCr  = 6.95 ± 2.15; cmIns  = 3.60 ± 0.74). CONCLUSION: A double-angulation acquisition enables improved metabolic characterization over a wide volume of the brain. J. Magn. Reson. Imaging 2015;42:280-289.
    Mots-clés : crmbm, snc.

  • Maarouf, Adil, Ferré, Jean-Christophe, Zaaraoui, Wafaa, Le Troter, Arnaud, Bannier, Elise, Berry, Isabelle, Guye, Maxime, et al. “Ultra-Small Superparamagnetic Iron Oxide Enhancement Is Associated With Higher Loss Of Brain Tissue Structure In Clinically Isolated Syndrome”. Multiple Sclerosis (Houndmills, Basingstoke, England). doi:10.1177/1352458515607649.
    Résumé : BACKGROUND: Macrophages are important components of inflammatory processes in multiple sclerosis, closely linked to axonal loss, and can now be observed in vivo using ultra-small superparamagnetic iron oxide (USPIO). In the present 1-year longitudinal study, we aimed to determine the prevalence and the impact on tissue injury of macrophage infiltration in patients after the first clinical event of multiple sclerosis. METHODS: Thirty-five patients, 32 years mean age, were imaged in a mean of 66 days after their first event using conventional magnetic resonance imaging, gadolinium (Gd) to probe blood-brain barrier integrity, USPIO to study macrophage infiltration and magnetization transfer ratio (MTR) to assess tissue structure integrity. Statistics were performed using two-group repeated-measures ANOVA. Any patient received treatment at baseline. RESULTS: At baseline, patients showed 17 USPIO-positive lesions reflecting infiltration of macrophages present from the onset. This infiltration was associated with local higher loss of tissue structure as emphasized by significant lower MTRnorm values (p<0.03) in USPIO(+)/Gd(+) lesions (n=16; MTRnormUSPIO(+)/Gd(+)=0.78 at baseline, MTRnormUSPIO(+)/Gd(+)=0.81 at M12) relative to USPIO(-)/Gd(+) lesions (n=67; MTRnormUSPIO(-)/Gd(+)=0.82 at baseline, MTRnormUSPIO(-)/Gd(+)=0.85 at M12). No interaction in MTR values was observed during the 12 months follow-up (lesion type × time). CONCLUSION: Infiltration of activated macrophages evidenced by USPIO enhancement, is present at the onset of multiple sclerosis and is associated with higher and persistent local loss of tissue structure. Macrophage infiltration affects more tissue structure while tissue recovery during the following year has a similar pattern for USPIO and Gd-enhanced lesions, leading to relative higher persistent local loss of tissue structure in lesions showing USPIO enhancement at baseline.

  • Ridley, Ben Gendon Yeshe, Rousseau, Celia, Wirsich, Jonathan, Le Troter, Arnaud, Soulier, Elisabeth, Confort-Gouny, Sylvianne, Bartolomei, Fabrice, Ranjeva, Jean-Philippe, Achard, Sophie, and Guye, Maxime. “Nodal Approach Reveals Differential Impact Of Lateralized Focal Epilepsies On Hub Reorganization”. Neuroimage 118: 39-48. doi:10.1016/j.neuroimage.2015.05.096.
    Résumé : The impact of the hemisphere affected by impairment in models of network disease is not fully understood. Among such models, focal epilepsies are characterised by recurrent seizures generated in epileptogenic areas also responsible for wider network dysfunction between seizures. Previous work focusing on functional connectivity within circumscribed networks suggests a divergence of network integrity and compensatory capacity between epilepsies as a function of the laterality of seizure onset. We evaluated the ability of complex network theory to reveal changes in focal epilepsy in global and nodal parameters using graph theoretical analysis of functional connectivity data obtained with resting-state fMRI. Graphs of functional connectivity networks were derived from 19 right and 13 left focal epilepsy patients and 15 controls. Topological metrics (degree, local efficiency, global efficiency and modularity) were computed for a whole-brain, atlas-defined network. We also calculated a hub disruption index for each graph metric, measuring the capacity of the brain network to demonstrate increased connectivity in some nodes for decreased connectivity in others. Our data demonstrate that the patient group as a whole is characterised by network-wide pattern of reorganization, even while global parameters fail to distinguish between groups. Furthermore, multiple metrics indicate that epilepsies with differently lateralized epileptic networks are asymmetric in their burden on functional brain networks; with left epilepsy patients being characterised by reduced efficiency and modularity, while in right epilepsy patients we provide the first evidence that functional brain networks are characterised by enhanced connectivity and efficiency at some nodes whereas reduced in others.
    Mots-clés : crmbm, Epilepsy, Functional connectivity, graph theory, Hemispheric asymmetry, Network modelling, resting-state, snc.

  • Taso, Manuel, Le Troter, Arnaud, Sdika, Michaël, Cohen-Adad, Julien, Arnoux, Pierre-Jean, Guye, Maxime, Ranjeva, Jean-Philippe, and Callot, Virginie. “A Reliable Spatially Normalized Template Of The Human Spinal Cord - Applications To Automated White Matter/gray Matter Segmentation And Tensor-Based Morphometry (Tbm) Mapping Of Gray Matter Alterations Occurring With Age”. Neuroimage 117: 20-28. doi:10.1016/j.neuroimage.2015.05.034.
    Résumé : Recently, a T2*-weighted template and probabilistic atlas of the white and gray matter (WM, GM) of the spinal cord (SC) have been reported. Such template can be used as tissue-priors for automated WM/GM segmentation but can also provide a common reference and normalized space for group studies. Here, a new template has been created (AMU40), and accuracy of automatic template-based WM/GM segmentation was quantified. The feasibility of tensor-based morphometry (TBM) for studying voxel-wise morphological differences of SC between young and elderly healthy volunteers was also investigated. Sixty-five healthy subjects were divided into young (n=40, age<40years old, mean age 28±5years old) and elderly (n=25, age>50years old, mean age 57±5years old) groups and scanned at 3T using an axial high-resolution T2*-weighted sequence. Inhomogeneity correction and affine intensity normalization of the SC and cerebrospinal fluid (CSF) signal intensities across slices were performed prior to both construction of the AMU40 template and WM/GM template-based segmentation. The segmentation was achieved using non-linear spatial normalization of T2*-w MR images to the AMU40 template. Validation of WM/GM segmentations was performed with a leave-one-out procedure by calculating DICE similarity coefficients between manual and automated WM/GM masks. SC morphological differences between young and elderly healthy volunteers were assessed using the same non-linear spatial normalization of the subjects' MRI to a common template, derivation of the Jacobian determinant maps from the warping fields, and a TBM analysis. Results demonstrated robust WM/GM automated segmentation, with mean DICE values greater than 0.8. Concerning the TBM analysis, an anterior GM atrophy was highlighted in elderly volunteers, demonstrating thereby, for the first time, the feasibility of studying local structural alterations in the SC using tensor-based morphometry. This holds great promise for studies of morphological impairment occurring in several central nervous system pathologies.
    Mots-clés : crmbm, snc.


Journal Article

  • Fonov, V. S., Le Troter, A., Taso, M., De Leener, B., Lévêque, G., Benhamou, M., Sdika, M., et al. “Framework For Integrated Mri Average Of The Spinal Cord White And Gray Matter: The Mni-Poly-Amu Template”. Neuroimage 102 Pt 2: 817-827. doi:10.1016/j.neuroimage.2014.08.057.
    Résumé : 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 (~15min), 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.
    Mots-clés : crmbm.

  • Fouré, Alexandre, Nosaka, Kazunori, Wegrzyk, Jennifer, Duhamel, Guillaume, Le Troter, Arnaud, Boudinet, Hélène, Mattei, Jean-Pierre, et al. “Time Course Of Central And Peripheral Alterations After Isometric Neuromuscular Electrical Stimulation-Induced Muscle Damage”. Plos One 9, no. 9: e107298. doi:10.1371/journal.pone.0107298.
    Résumé : Isometric contractions induced by neuromuscular electrostimulation (NMES) have been shown to result in a prolonged force decrease but the time course of the potential central and peripheral factors have never been investigated. This study examined the specific time course of central and peripheral factors after isometric NMES-induced muscle damage. Twenty-five young healthy men were subjected to an NMES exercise consisting of 40 contractions for both legs. Changes in maximal voluntary contraction force of the knee extensors (MVC), peak evoked force during double stimulations at 10 Hz (Db10) and 100 Hz (Db100), its ratio (10∶100), voluntary activation, muscle soreness and plasma creatine kinase activity were assessed before, immediately after and throughout four days after NMES session. Changes in knee extensors volume and T2 relaxation time were also assessed at two (D2) and four (D4) days post-exercise. MVC decreased by 29% immediately after NMES session and was still 19% lower than the baseline value at D4. The decrease in Db10 was higher than in Db100 immediately and one day post-exercise resulting in a decrease (-12%) in the 10∶100 ratio. On the contrary, voluntary activation significantly decreased at D2 (-5%) and was still depressed at D4 (-5%). Muscle soreness and plasma creatine kinase activity increased after NMES and peaked at D2 and D4, respectively. T2 was also increased at D2 (6%) and D4 (9%). Additionally, changes in MVC and peripheral factors (e.g., Db100) were correlated on the full recovery period, while a significant correlation was found between changes in MVC and VA only from D2 to D4. The decrease in MVC recorded immediately after the NMES session was mainly due to peripheral changes while both central and peripheral contributions were involved in the prolonged force reduction. Interestingly, the chronological events differ from what has been reported so far for voluntary exercise-induced muscle damage.
    Mots-clés : Adult, crmbm, Electric Stimulation, Electromyography, Exercise, Humans, Isometric Contraction, Knee, Male, Muscle Contraction, Muscle Fatigue, Neuromuscular Diseases.

  • Maarouf, Adil, Audoin, Bertrand, Konstandin, Simon, Rico, Audrey, Soulier, Elisabeth, Reuter, Françoise, Troter, Arnaud Le, et al. “Topography Of Brain Sodium Accumulation In Progressive Multiple Sclerosis”. Magnetic Resonance Materials In Physics, Biology And Medicine 27, no. 1: 53-62. doi:10.1007/s10334-013-0396-1.
    Résumé : Object Sodium accumulation is involved in neuronal injury occurring in multiple sclerosis (MS). We aimed to assess sodium accumulation in progressive MS, known to suffer from severe neuronal injury. Materials and methods 3D-23Na-MRI was obtained on a 3T-MR-scanner in 20 progressive MS patients [11 primary-progressive (PPMS) and nine secondary-progressive (SPMS)] and 15 controls. Total sodium concentrations (TSC) within grey matter (GM), normal-appearing white matter (WM) and lesions were extracted. Statistical mapping analyses of TSC abnormalities were also performed. Results Progressive MS patients presented higher GM–TSC values (48.8 ± 3.1 mmol/l wet tissue vol, p < 0.001) and T2lesions-TSC values (50.9 ± 2.2 mmol/l wet tissue vol, p = 0.01) compared to GM and WM of controls. Statistical mapping analysis showed TSC increases in PPMS patients confined to motor and somatosensory cortices, prefrontal cortices, pons and cerebellum. In SPMS, TSC increases were associated with areas involving: primary motor, premotor and somatosensory cortices; prefrontal, cingulate and visual cortices; the corpus callosum, thalami, brainstem and cerebellum. Anterior prefrontal and premotor cortices TSC were correlated with disability. Conclusion Sodium accumulation is present in progressive MS patients, more restricted to the motor system in PPMS and more widespread in SPMS. Local brain sodium accumulation appears as a promising marker to monitor patients with progressive MS.
    Mots-clés : Adult, Aged, Biomedical Engineering, Brain, Brain Mapping, Case-Control Studies, Computer Appl. in Life Sciences, crmbm, Disability, Female, Grey matter, Health Informatics, Humans, Imaging / Radiology, Magnetic Resonance Imaging, Male, Middle Aged, MRI, Multiple sclerosis, Nerve Fibers, Myelinated, Neurons, Progressive multiple sclerosis, Sodium, Solid State Physics.

  • Taso, Manuel, Le Troter, Arnaud, Sdika, Michaël, Ranjeva, Jean-Philippe, Guye, Maxime, Bernard, Monique, and Callot, Virginie. “Construction Of An In Vivo Human Spinal Cord Atlas Based On High-Resolution Mr Images At Cervical And Thoracic Levels: Preliminary Results”. Magma (New York, N.y.) 27, no. 3: 257-267. doi:10.1007/s10334-013-0403-6.
    Résumé : OBJECT: Our goal was to build a probabilistic atlas and anatomical template of the human cervical and thoracic spinal cord (SC) that could be used for segmentation algorithm improvement, parametric group studies, and enrichment of biomechanical modelling. MATERIALS AND METHODS: High-resolution axial T2*-weighted images were acquired at 3T on 15 healthy volunteers using a multi-echo-gradient-echo sequence (1 slice per vertebral level from C1 to L2). After manual segmentation, linear and affine co-registrations were performed providing either inter-individual morphometric variability maps, or substructure probabilistic maps [CSF, white and grey matter (WM/GM)] and anatomical SC template. RESULTS: The larger inter-individual morphometric variations were observed at the thoraco-lumbar levels and in the posterior GM. Mean SC diameters were in agreement with the literature and higher than post-mortem measurements. A representative SC MR template was generated and values up to 90 and 100% were observed on GM and WM-probability maps. CONCLUSION: This work provides a probabilistic SC atlas and a template that could offer great potentialities for parametrical MRI analysis (DTI/MTR/fMRI) and group studies, similar to what has already been performed using a brain atlas. It also offers great perspective for biomechanical models usually based on post-mortem or generic data. Further work will consider integration into an automated SC segmentation pipeline.
    Mots-clés : award_ESMRMB13, crmbm.

  • Wirsich, Jonathan, Bénar, Christian, Ranjeva, Jean-Philippe, Descoins, Médéric, Soulier, Elisabeth, Le Troter, Arnaud, Confort-Gouny, Sylviane, Liégeois-Chauvel, Catherine, and Guye, Maxime. “Single-Trial Eeg-Informed Fmri Reveals Spatial Dependency Of Bold Signal On Early And Late Ic-Erp Amplitudes During Face Recognition”. Neuroimage 100: 325-336. doi:10.1016/j.neuroimage.2014.05.075.
    Résumé : Simultaneous EEG-fMRI has opened up new avenues for improving the spatio-temporal resolution of functional brain studies. However, this method usually suffers from poor EEG quality, especially for evoked potentials (ERPs), due to specific artifacts. As such, the use of EEG-informed fMRI analysis in the context of cognitive studies has particularly focused on optimizing narrow ERP time windows of interest, which ignores the rich diverse temporal information of the EEG signal. Here, we propose to use simultaneous EEG-fMRI to investigate the neural cascade occurring during face recognition in 14 healthy volunteers by using the successive ERP peaks recorded during the cognitive part of this process. N170, N400 and P600 peaks, commonly associated with face recognition, were successfully and reproducibly identified for each trial and each subject by using a group independent component analysis (ICA). For the first time we use this group ICA to extract several independent components (IC) corresponding to the sequence of activation and used single-trial peaks as modulation parameters in a general linear model (GLM) of fMRI data. We obtained an occipital–temporal–frontal stream of BOLD signal modulation, in accordance with the three successive IC-ERPs providing an unprecedented spatio-temporal characterization of the whole cognitive process as defined by BOLD signal modulation. By using this approach, the pattern of EEG-informed BOLD modulation provided improved characterization of the network involved than the fMRI-only analysis or the source reconstruction of the three ERPs; the latter techniques showing only two regions in common localized in the occipital lobe.
    Mots-clés : crmbm, Evoked Potentials, Face recognition, ICA, Simultaneous EEG-fMRI, Ventral visual pathway.


Conference Paper
  • Coulon, Olivier, Auzias, Guillaume, Le Troter, Arnaud, Operto, Grégory, and Rivière, Denis. “Cortical Surface : A Brainvisa Toolbox For Surface-Based Processing Of Neuroimaging Data”. In, Seattle, WA, USA, 2013.
  • Leporq, Benjamin, Le Troter, Arnaud, Le Fur, Yann, Salort-Campana, Emmanuelle, Cozzone, Patrick, Beuf, Olivier, and Bendahan, David. “Combination Of A Fat Volume Fraction Quantification Method With A Dedicated Automatic Segmentation Algorithm For Simultaneous Measurement Of Infiltrated Fatty Tissue Fraction And Muscle Relaxation Times.”. In, Salt Lake City, Utah, USA, 2013.
    Résumé : Due to its sensitivity to key processes in the diseased muscle such oedema, inflammation and fatty infiltration, MRI is emerging as a suitable quantitative method which could provide reliable surrogate markers of disease severity and progression. This work investigates the feasibility of a method to distinguish IMAT and SCAT, (ii) to measure muscle relaxation times (T1 andT2*) and to quantify the infiltrated fatty tissue fraction (IFTF) simultaneously. Our approach includes a magnitude-based fat volume fraction quantification method based on multiple-echo multiple angle acquisition with a dedicated automatic segmentation algorithm.
Journal Article

  • Auzias, G, Lefevre, J, Le Troter, A, Fischer, C, Perrot, M, Regis, J, and Coulon, O. “Model-Driven Harmonic Parameterization Of The Cortical Surface: Hip-Hop”. Ieee Transactions On Medical Imaging 32, no. 5: 873-887. doi:10.1109/TMI.2013.2241651.
    Résumé : In the context of inter subject brain surface matching, we present a parameterization of the cortical surface constrained by a model of cortical organization. The parameterization is defined via an harmonic mapping of each hemisphere surface to a rectangular planar domain that integrates a representation of the model. As opposed to previous landmark-based registration methods we do not match folds between individuals but instead optimize the fit between cortical sulci and specific iso-coordinate axis in the model. This strategy overcomes some limitation to sulcus-based registration techniques such as topological variability in sulcal landmarks across subjects. Experiments on 62 subjects with manually traced sulci are presented and compared with the result of the Freesurfer software. The evaluation involves a measure of dispersion of sulci with both angular and area distortions. We show that the model-based strategy can lead to a natural, efficient and very fast (less than 5 min per hemisphere) method for defining inter subjects correspondences. We discuss how this approach also reduces the problems inherent to anatomically defined landmarks and open the way to the investigation of cortical organization through the notion of orientation and alignment of structures across the cortex.

  • Conductier, Grégory, Viola, Angèle, le Troter, Arnaud, Nahon, Jean-Louis, and Guyon, Alice. “[Beating Frequency Of Motile Cilia Lining The Third Cerebral Ventricle Is Finely Tuned By The Hypothalamic Peptide Mch]”. Médecine Sciences: M/s 29, no. 11: 943-945. doi:10.1051/medsci/20132911004.

  • Gineste, Charlotte, Le Fur, Yann, Vilmen, Christophe, Le Troter, Arnaud, Pecchi, Emilie, Cozzone, Patrick J, Hardeman, Edna C, Bendahan, David, and Gondin, Julien. “Combined Mri And (31)P-Mrs Investigations Of The Acta1(H40Y) Mouse Model Of Nemaline Myopathy Show Impaired Muscle Function And Altered Energy Metabolism”. Plos One 8, no. 4: e61517. doi:10.1371/journal.pone.0061517.
    Résumé : Nemaline myopathy (NM) is the most common disease entity among non-dystrophic skeletal muscle congenital diseases. Mutations in the skeletal muscle α-actin gene (ACTA1) account for ∼25% of all NM cases and are the most frequent cause of severe forms of NM. So far, the mechanisms underlying muscle weakness in NM patients remain unclear. Additionally, recent Magnetic Resonance Imaging (MRI) studies reported a progressive fatty infiltration of skeletal muscle with a specific muscle involvement in patients with ACTA1 mutations. We investigated strictly noninvasively the gastrocnemius muscle function of a mouse model carrying a mutation in the ACTA1 gene (H40Y). Skeletal muscle anatomy (hindlimb muscles and fat volumes) and energy metabolism were studied using MRI and (31)Phosphorus magnetic resonance spectroscopy. Skeletal muscle contractile performance was investigated while applying a force-frequency protocol (from 1-150 Hz) and a fatigue protocol (80 stimuli at 40 Hz). H40Y mice showed a reduction of both absolute (-40%) and specific (-25%) maximal force production as compared to controls. Interestingly, muscle weakness was associated with an improved resistance to fatigue (+40%) and an increased energy cost. On the contrary, the force frequency relationship was not modified in H40Y mice and the extent of fatty infiltration was minor and not different from the WT group. We concluded that the H40Y mouse model does not reproduce human MRI findings but shows a severe muscle weakness which might be related to an alteration of intrinsic muscular properties. The increased energy cost in H40Y mice might be related to either an impaired mitochondrial function or an alteration at the cross-bridges level. Overall, we provided a unique set of anatomic, metabolic and functional biomarkers that might be relevant for monitoring the progression of NM disease but also for assessing the efficacy of potential therapeutic interventions at a preclinical level.
    Mots-clés : Actins, Animals, crmbm, Energy Metabolism, Female, Magnetic Resonance Imaging, Mice, Mice, Mutant Strains, Muscle, Skeletal, Myopathies, Nemaline.


Conference Paper

  • Operto, Grégory, Auzias, Guillaume, Le Troter, Arnaud, Perrot, Matthieu, Rivière, Denis, Dubois, Jessica, Hüppi, Petra, Coulon, Olivier, and Mangin, jean-francois. “Structural Group Analysis Of Cortical Curvature And Depth Patterns In The Developing Brain”. In, 422-425, Barcelona, 2012.
    Résumé : In the context of the study of brain morphogenesis, we present here a framework for surface-based group analysis using local cortical features in the neonate brain. We propose to detect and match local maxima from curvature and depth profiles of sulcal fundi. Such entities could have a key role to understand the variability of the brain morphology. We also describe a cortical localization tool dedicated to the developing brain. The proposed method is performed on a dataset of 25 preterm newborns and has detected consistent entities at the group level, both from cortical curvature and depth maps.
  • Wazaefi, Yanal, Bruneu, Yvane, Lefevre, Julien, Menegaz, Gloria, Paggetti, Giullia, Le Troter, Arnaud, Paris, Sébastien, Grob, Jean-jacques, and Fertil, Bernard. “Consensus Clustering From Experts' Partitions For Patients' Nevi: Model The Ugly Duckling”. In, Las Vegas, Nevada, USA, 2012.
    Résumé : Ugly duckling (UD) concept assumes that nevi in the same patient tend to share some morphological features so that dermatologists identify a few similarity clusters. UD is the nevus that does not fit into any of those clusters, likely to be suspicious. Our research program was to model the ability of dermatologists to identify the perceived similarity clusters (PSC) as an additional tool for computer-aided melanoma diagnosis systems. In the present study, nine dermatologists participated to do the clustering of nevi and to identify the UDs using dermoscopic images of nevi of 80 individuals. Dermatologists identified all confirmed melanomas as UDs and tend to be concordant about the identification of PSCs. We combined the multiple clusterings of dermatologists to find the consensus clustering, which yields a stable and robust final clustering. We demonstrated the limited variability of nevi patterns per individual (2.45 PSCs in average), whatever the number of nevi, which human brain has a natural intuitive ability to perceive
Journal Article

  • Le Troter, A, Auzias, G, and Coulon, O. “Automatic Sulcal Line Extraction On Cortical Surfaces Using Geodesic Path Density Maps”. Neuroimage 61, no. 4: 941-949. doi:10.1016/j.neuroimage.2012.04.021.
    Résumé : We present here a method that is designed to automatically extract sulcal lines on the mesh of any cortical surface. The method is based on the definition of a new function, the Geodesic Path Density Map (GPDM), within each sulcal basin (i.e. regions with a negative mean curvature). GPDM indicates at each vertex the likelihood that a shortest path between any two points of the basins boundary goes through that vertex. If the distance used to compute shortest path is anisotropic and constrained by a geometric information such as the depth, the GPDM indicates the likelihood that a vertex belongs to the sulcal line in the basin. An automatic GPDM adaptive thresholding procedure is proposed and sulcal lines are then defined. The process has been validated on a set of 25 subjects by comparing results to the manual segmentation from an expert and showed an average error below 2mm. It is also compared to our previous reference method in the context of inter-subject cortical surface registration and shows an significant improvement in performance.
    Mots-clés : Algorithms, Brain Mapping, Cerebral Cortex, crmbm, Humans, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional.


Conference Paper
  • Auzias, Guillaume, Lefevre, Julien, Le Troter, Arnaud, Régis, Jean, and Coulon, Olivier. “Model-Driven Conformal Parameterization Of The Cortical Surface”. In, 6892:310-317, 2011.

  • Le Troter, Arnaud, Auzias, Guillaume, and Coulon, Olivier. “Automatic Extraction Of Sulcal Lines On The Cortical Surface Using Shortest Path Probability Maps”. In, 2011:5165-5168, 2011. doi:10.1109/IEMBS.2011.6091279.
    Résumé : This paper describes an automatic procedure for extracting sulcal lines from cortical surface meshes of the human brain, which will serve as a tool for landmark extraction as well as for investigating the morphometry of sulci. The procedure consists in a sequence of steps, including sulcal basin segmentation based on local curvature information, estimating a bundle of depth-constrained geodesic paths and determining a robust probability map of sulcal lines crossing. In this experiment, we present quantitative validations on two main sulci to observe the agreement of our method with manually traced curves.
    Mots-clés : Algorithms, Cerebral Cortex, Data Interpretation, Statistical, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity.
  • Le Troter, Arnaud, Rivière, D, and Coulon, O. “An Interactive Sulcal Fundi Editor In Brainvisa”. In, 2011.


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