Keyword search (3,448 papers available)


File-based localization of numerical perturbations in data analysis pipelines.

Author(s): Salari A, Kiar G, Lewis L, Evans AC, Glatard T

BACKGROUND: Data analysis pipelines are known to be affected by computational conditions, presumably owing to the creation and propagation of numerical errors. While this process could play a major role in the current reproducibility crisis, the precise cau...

Article GUID: 33269388
Comparing perturbation models for evaluating stability of neuroimaging pipelines.

Author(s): Kiar G, de Oliveira Castro P, Rioux P, Petit E, Brown ST, Evans AC, Glatard T

With an increase in awareness regarding a troubling lack of reproducibility in analytical software tools, the degree of validity in scientific derivatives and their downstream results has become unclear. The nature of reproducibility issues may vary across ...

Article GUID: 32831546
Cyberinfrastructure for Open Science at the Montreal Neurological Institute.

Author(s): Das S, Glatard T, Rogers C, Saigle J, Paiva S, MacIntyre L, Safi-Harab M, Rousseau ME, Stirling J, Khalili-Mahani N, MacFarlane D, Kostopoul...

Front Neuroinform. 2016;10:53 Authors: 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, Ma...

Article GUID: 28111547
Best practices in data analysis and sharing in neuroimaging using MRI.

Author(s): 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 Ess...

Nat Neurosci. 2017 Feb 23;20(3):299-303 Authors: 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, ...

Article GUID: 28230846
Boutiques: a flexible framework to integrate command-line applications in computing platforms.

Author(s): 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...

Gigascience. 2018 05 01;7(5): Authors: 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...

Article GUID: 29718199
A Serverless Tool for Platform Agnostic Computational Experiment Management.

Author(s): Kiar G, Brown ST, Glatard T, Evans AC

Front Neuroinform. 2019;13:12 Authors: Kiar G, Brown ST, Glatard T, Evans AC

Article GUID: 30890927
Biomarkers, designs, and interpretations of resting-state fMRI in translational pharmacological research: A review of state-of-the-Art, challenges, and opportunities for studying brain chemistry.

Author(s): Khalili-Mahani N, Rombouts SA, van Osch MJ, Duff EP, Carbonell F, Nickerson LD, Becerra L, Dahan A, Evans AC, Soucy JP, Wise R, Zijdenbos AP...

Hum Brain Mapp. 2017 04;38(4):2276-2325 Authors: Khalili-Mahani N, Rombouts SA, van Osch MJ, Duff EP, Carbonell F, Nickerson LD, Becerra L, Dahan A, Evans AC, Soucy JP, Wise R, Zijdenbos AP, van G...

Article GUID: 28145075
Title:Biomarkers, designs, and interpretations of resting-state fMRI in translational pharmacological research: A review of state-of-the-Art, challenges, and opportunities for studying brain chemistry.
Authors:Khalili-Mahani N,  Rombouts SA,  van Osch MJ,  Duff EP,  Carbonell F,  Nickerson LD,  Becerra L,  Dahan A,  Evans AC,  Soucy JP,  Wise R,  Zijdenbos AP,  van Gerven JM
Link:https://www.ncbi.nlm.nih.gov/pubmed/28145075?dopt=Abstract
DOI:10.1002/hbm.23516
Category:Hum Brain Mapp
PMID:28145075
Dept Affiliation: PERFORM
1 McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montreal, Canada.
2 PERFORM Centre, Concordia University, Montreal, Canada.
3 Department of Radiology, Leiden University Medical Centre, Leiden, The Netherlands.
4 Institute of Psychology and Leiden Institute for Brain and Cognition, Leiden University, Leiden, The Netherlands.
5 Oxford Centre for Functional MRI of the Brain, Oxford University, Oxford, United Kingdom.
6 Biospective Inc, Montreal, Quebec, Canada.
7 McLean Hospital, Belmont, Massachusetts.
8 Harvard Medical School, Boston, Massachusetts.
9 Center for Pain and the Brain, Harvard Medical School & Boston Children's Hospital, Boston, Massachusetts.
10 Department of Anesthesiology, Leiden University Medical Centre, Leiden, The Netherlands.
11 McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada.
12 Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom.
13 Centre for Human Drug Research, Leiden University Medical Centre, Leiden, The Netherlands.

Description:

Biomarkers, designs, and interpretations of resting-state fMRI in translational pharmacological research: A review of state-of-the-Art, challenges, and opportunities for studying brain chemistry.

Hum Brain Mapp. 2017 04;38(4):2276-2325

Authors: Khalili-Mahani N, Rombouts SA, van Osch MJ, Duff EP, Carbonell F, Nickerson LD, Becerra L, Dahan A, Evans AC, Soucy JP, Wise R, Zijdenbos AP, van Gerven JM

Abstract

A decade of research and development in resting-state functional MRI (RSfMRI) has opened new translational and clinical research frontiers. This review aims to bridge between technical and clinical researchers who seek reliable neuroimaging biomarkers for studying drug interactions with the brain. About 85 pharma-RSfMRI studies using BOLD signal (75% of all) or arterial spin labeling (ASL) were surveyed to investigate the acute effects of psychoactive drugs. Experimental designs and objectives include drug fingerprinting dose-response evaluation, biomarker validation and calibration, and translational studies. Common biomarkers in these studies include functional connectivity, graph metrics, cerebral blood flow and the amplitude and spectrum of BOLD fluctuations. Overall, RSfMRI-derived biomarkers seem to be sensitive to spatiotemporal dynamics of drug interactions with the brain. However, drugs cause both central and peripheral effects, thus exacerbate difficulties related to biological confounds, structured noise from motion and physiological confounds, as well as modeling and inference testing. Currently, these issues are not well explored, and heterogeneities in experimental design, data acquisition and preprocessing make comparative or meta-analysis of existing reports impossible. A unifying collaborative framework for data-sharing and data-mining is thus necessary for investigating the commonalities and differences in biomarker sensitivity and specificity, and establishing guidelines. Multimodal datasets including sham-placebo or active control sessions and repeated measurements of various psychometric, physiological, metabolic and neuroimaging phenotypes are essential for pharmacokinetic/pharmacodynamic modeling and interpretation of the findings. We provide a list of basic minimum and advanced options that can be considered in design and analyses of future pharma-RSfMRI studies. Hum Brain Mapp 38:2276-2325, 2017. © 2017 Wiley Periodicals, Inc.

PMID: 28145075 [PubMed - indexed for MEDLINE]