Keyword search (4,163 papers available)

"Glatard T" Authored Publications:

Title Authors PubMed ID
1 Hierarchical Storage Management in User Space for Neuroimaging Applications Hayot-Sasson V; Glatard T; 41432812
ENCS
2 Open-source platforms to investigate analytical flexibility in neuroimaging Sanz-Robinson J; Wang M; McPherson B; Chatelain Y; Kennedy D; Glatard T; Poline JB; 40800896
ENCS
3 An analysis of performance bottlenecks in MRI preprocessing Dugré M; Chatelain Y; Glatard T; 40072903
ENCS
4 Predicting Parkinson's disease trajectory using clinical and functional MRI features: A reproduction and replication study Germani E; Bhagwat N; Dugré M; Gau R; Montillo AA; Nguyen KP; Sokolowski A; Sharp M; Poline JB; Glatard T; 39982930
ENCS
5 Registered report: Age-preserved semantic memory and the CRUNCH effect manifested as differential semantic control networks: An fMRI study Haitas N; Dubuc J; Massé-Leblanc C; Chamberland V; Amiri M; Glatard T; Wilson M; Joanette Y; Steffener J; 38917084
ENCS
6 Longitudinal brain structure changes in Parkinson's disease: A replication study Sokolowski A; Bhagwat N; Chatelain Y; Dugré M; Hanganu A; Monchi O; McPherson B; Wang M; Poline JB; Sharp M; Glatard T; 38295031
ENCS
7 Numerical stability of DeepGOPlus inference Gonzalez Pepe I; Chatelain Y; Kiar G; Glatard T; 38285635
ENCS
8 Data and Tools Integration in the Canadian Open Neuroscience Platform Poline JB; Das S; Glatard T; Madjar C; Dickie EW; Lecours X; Beaudry T; Beck N; Behan B; Brown ST; Bujold D; Beauvais M; Caron B; Czech C; Dharsee M; Dugré M; Evans K; Gee T; Ippoliti G; Kiar G; Knoppers BM; Kuehn T; Le D; Lo D; Mazaheri M; MacFarlane D; Muja N; O' Brien EA; O' Callaghan L; Paiva S; Park P; Quesnel D; Rabelais H; Rioux P; Legault M; Tremblay-Mercier J; Rotenberg D; Stone J; Strauss T; Zaytseva K; Zhou J; Duchesne S; Khan AR; Hill S; Evans AC; 37024500
ENCS
9 Numerical uncertainty in analytical pipelines lead to impactful variability in brain networks Kiar G; Chatelain Y; de Oliveira Castro P; Petit E; Rokem A; Varoquaux G; Misic B; Evans AC; Glatard T; 34724000
ENCS
10 Multiple sclerosis lesions segmentation from multiple experts: the MICCAI 2016 challenge dataset Commowick O; Kain M; Casey R; Ameli R; Ferré JC; Kerbrat A; Tourdias T; Cervenansky F; Camarasu-Pop S; Glatard T; Vukusic S; Edan G; Barillot C; Dojat M; Cotton FI; 34563682
ENCS
11 The BigBrainWarp toolbox for integration of BigBrain 3D histology with multimodal neuroimaging Paquola C; Royer J; Lewis LB; Lepage C; Glatard T; Wagstyl K; DeKraker J; Toussaint PJ; Valk SL; Collins DL; Khan A; Amunts K; Evans AC; Dickscheid T; Bernhardt BC; 34431476
IMAGING
12 An analysis of security vulnerabilities in container images for scientific data analysis Kaur B; Dugré M; Hanna A; Glatard T; 34080631
ENCS
13 File-based localization of numerical perturbations in data analysis pipelines. Salari A, Kiar G, Lewis L, Evans AC, Glatard T 33269388
ENCS
14 A Benchmark of Data Stream Classification for Human Activity Recognition on Connected Objects. Khannouz M; Glatard T; 33202905
ENCS
15 Comparing perturbation models for evaluating stability of neuroimaging pipelines. Kiar G, de Oliveira Castro P, Rioux P, Petit E, Brown ST, Evans AC, Glatard T 32831546
IMAGING
16 A Quantitative Comparison of Overlapping and Non-Overlapping Sliding Windows for Human Activity Recognition Using Inertial Sensors. Dehghani A, Sarbishei O, Glatard T, Shihab E 31752158
ENCS
17 Cyberinfrastructure for Open Science at the Montreal Neurological Institute. Das S, Glatard T, Rogers C, Saigle J, Paiva S, MacIntyre L, Safi-Harab M, Rousseau ME, Stirling J, Khalili-Mahani N, MacFarlane D, Kostopoulos P, Rioux P, Madjar C, Lecours-Boucher X, Vanamala S, Adalat R, Mohaddes Z, Fonov VS, Milot S, Leppert I, Degroot C, Durcan TM, Campbell T, Moreau J, Dagher A, Collins DL, Karamchandani J, Bar-Or A, Fon EA, Hoge R, Baillet S, Rouleau G, Evans AC 28111547
IMAGING
18 Best practices in data analysis and sharing in neuroimaging using MRI. Nichols TE, Das S, Eickhoff SB, Evans AC, Glatard T, Hanke M, Kriegeskorte N, Milham MP, Poldrack RA, Poline JB, Proal E, Thirion B, Van Essen DC, White T, Yeo BT 28230846
IMAGING
19 The first MICCAI challenge on PET tumor segmentation. Hatt M, Laurent B, Ouahabi A, Fayad H, Tan S, Li L, Lu W, Jaouen V, Tauber C, Czakon J, Drapejkowski F, Dyrka W, Camarasu-Pop S, Cervenansky F, Girard P, Glatard T, Kain M, Yao Y, Barillot C, Kirov A, Visvikis D 29268169
IMAGING
20 Boutiques: a flexible framework to integrate command-line applications in computing platforms. Glatard T, Kiar G, Aumentado-Armstrong T, Beck N, Bellec P, Bernard R, Bonnet A, Brown ST, Camarasu-Pop S, Cervenansky F, Das S, Ferreira da Silva R, Flandin G, Girard P, Gorgolewski KJ, Guttmann CRG, Hayot-Sasson V, Quirion PO, Rioux P, Rousseau MÉ, Evans AC 29718199
ENCS
21 Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure. Commowick O, Istace A, Kain M, Laurent B, Leray F, Simon M, Pop SC, Girard P, Améli R, Ferré JC, Kerbrat A, Tourdias T, Cervenansky F, Glatard T, Beaumont J, Doyle S, Forbes F, Knight J, Khademi A, Mahbod A, Wang C, McKinley R, Wagner F, Muschelli J, Sweeney E, Roura E, Lladó X, Santos MM, Santos WP, Silva-Filho AG, Tomas-Fernandez X, Urien H, Bloch I, Valverde S, Cabezas M, Vera-Olmos FJ, Malpica N, Guttmann C, Vukusic S, Edan G, Dojat M, Styner M, Warfield SK, Cotton F, Barillot C 30209345
ENCS
22 A Serverless Tool for Platform Agnostic Computational Experiment Management. Kiar G, Brown ST, Glatard T, Evans AC 30890927
ENCS

 

Title:Numerical uncertainty in analytical pipelines lead to impactful variability in brain networks
Authors:Kiar GChatelain Yde Oliveira Castro PPetit ERokem AVaroquaux GMisic BEvans ACGlatard T
Link:pubmed.ncbi.nlm.nih.gov/34724000/
DOI:10.1371/journal.pone.0250755
Publication:PloS one
Keywords:
PMID:34724000 Category: Date Added:2021-11-01
Dept Affiliation: ENCS
1 Montréal Neurological Institute, McGill University, Montréal, QC, Canada.
2 Department of Computer Science and Software Engineering, Concordia University, Montréal, QC, Canada.
3 Department of Computer Science, Université of Versailles, Versailles, France.
4 Exascale Computing Lab, Intel, Paris, France.
5 Department of Psychology and eScience Institute, University of Washington, Seattle, WA, United States of America.
6 Parietal Project-team, INRIA Saclay-ile de France, Paris, France.

Description:

The analysis of brain-imaging data requires complex processing pipelines to support findings on brain function or pathologies. Recent work has shown that variability in analytical decisions, small amounts of noise, or computational environments can lead to substantial differences in the results, endangering the trust in conclusions. We explored the instability of results by instrumenting a structural connectome estimation pipeline with Monte Carlo Arithmetic to introduce random noise throughout. We evaluated the reliability of the connectomes, the robustness of their features, and the eventual impact on analysis. The stability of results was found to range from perfectly stable (i.e. all digits of data significant) to highly unstable (i.e. 0 - 1 significant digits). This paper highlights the potential of leveraging induced variance in estimates of brain connectivity to reduce the bias in networks without compromising reliability, alongside increasing the robustness and potential upper-bound of their applications in the classification of individual differences. We demonstrate that stability evaluations are necessary for understanding error inherent to brain imaging experiments, and how numerical analysis can be applied to typical analytical workflows both in brain imaging and other domains of computational sciences, as the techniques used were data and context agnostic and globally relevant. Overall, while the extreme variability in results due to analytical instabilities could severely hamper our understanding of brain organization, it also affords us the opportunity to increase the robustness of findings.




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