Seven quick tips for analysis scripts in neuroimaging

Vliet, Marijn van

doi:10.1371/journal.pcbi.1007358

Cited by 15 publications

(17 citation statements)

References 27 publications

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“…MEG data were analyzed further using custom scripting [ 21 ] of the MNE-Python software package [ 22 , 23 ]. First, the MEG signals were high-pass filtered at 1 Hz and independent component analysis was used to suppress ocular artefacts; the independent components correlating most with the EOG signal were removed.…”

Section: Methodsmentioning

confidence: 99%

Effect of long-term paired associative stimulation on the modulation of cortical sensorimotor oscillations after spinal cord injury

Vanhanen

Parkkonen

Mäkelä

et al. 2022

Spinal Cord Ser Cases

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Study design A prospective interventional case series. Objectives To explore changes in the modulation of cortical sensorimotor oscillations after long-term paired associative stimulation (PAS) in participants with spinal cord injury (SCI). Setting BioMag Laboratory, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland. Methods Five patients with chronic incomplete SCI received unilateral spinal PAS to upper limb for 16–22 days. Changes in the modulation of sensorimotor oscillations in response to tactile stimulus and active and imaginary hand movements were assessed with magnetoencephalography recorded before and after the intervention. Results PAS restored the modulation of sensorimotor oscillations in response to active hand movement in four patients, whereas the modulation following tactile stimulation remained unaltered. The observed change was larger in the hemisphere that received PAS and preceded the clinical effect of the intervention. Conclusions Long-term spinal PAS treatment, which enhances the motor functions of SCI patients, also restores the modulation of cortical sensorimotor oscillations.

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Section: Methodsmentioning

confidence: 99%

Effect of long-term paired associative stimulation on the modulation of cortical sensorimotor oscillations after spinal cord injury

Vanhanen

Parkkonen

Mäkelä

et al. 2022

Spinal Cord Ser Cases

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“…Therefore, the programming code itself becomes the most accurate source of the exact analysis steps performed on the data, and is anyway needed for reproducibility. Thus, it needs to be organized and clear (see recommendations suggested by Sandve et al 2013;van Vliet 2020;Wilson et al 2017), otherwise, results may not be reproducible, or even correct (Casadevall and Fang 2014;Pavlov et al 2021). It should be noted that sharing an imperfect code is still much better than not sharing at all (Barnes 2010;Gorgolewski and Poldrack 2016).…”

Section: Methodological Transparencymentioning

confidence: 99%

Open and reproducible neuroimaging: from study inception to publication

Niso¹,

Botvinik‐Nezer²,

Appelhoff³

et al. 2022

Preprint

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Empirical observations of how labs conduct research indicate that the adoption rate of open practices for transparent, reproducible, and collaborative science remains in its infancy. This is at odds with the overwhelming evidence for the necessity of these practices and their benefits for individual researchers, scientific progress, and society in general. To date, information required for implementing open science practices throughout the different steps of a research project is scattered among many different sources. Even experienced researchers in the topic find it hard to navigate the ecosystem of tools and to make sustainable choices. Here, we provide an integrated overview of community-developed resources that can support collaborative, open, and reproducible neuroimaging throughout the entire research cycle from inception to publication and across different neuroimaging modalities. We review tools and practices supporting study inception and planning, data acquisition, research data management, data processing and analysis, and research dissemination. We believe it will prove helpful for researchers and institutions to make a successful and sustainable move towards open and reproducible science and to eventually take an active role in its future development.

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“…The design of the RiboViz Python script follows the majority of van Vliet’s 7 quick tips for analysis scripts [ 16 ], tips which are generally applicable beyond neuroimaging. The development of RiboViz has also been strongly guided by Wilson and colleagues’ best practices for scientific computing [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Using prototyping to choose a bioinformatics workflow management system

2021

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Workflow management systems represent, manage, and execute multistep computational analyses and offer many benefits to bioinformaticians. They provide a common language for describing analysis workflows, contributing to reproducibility and to building libraries of reusable components. They can support both incremental build and re-entrancy—the ability to selectively re-execute parts of a workflow in the presence of additional inputs or changes in configuration and to resume execution from where a workflow previously stopped. Many workflow management systems enhance portability by supporting the use of containers, high-performance computing (HPC) systems, and clouds. Most importantly, workflow management systems allow bioinformaticians to delegate how their workflows are run to the workflow management system and its developers. This frees the bioinformaticians to focus on what these workflows should do, on their data analyses, and on their science. RiboViz is a package to extract biological insight from ribosome profiling data to help advance understanding of protein synthesis. At the heart of RiboViz is an analysis workflow, implemented in a Python script. To conform to best practices for scientific computing which recommend the use of build tools to automate workflows and to reuse code instead of rewriting it, the authors reimplemented this workflow within a workflow management system. To select a workflow management system, a rapid survey of available systems was undertaken, and candidates were shortlisted: Snakemake, cwltool, Toil, and Nextflow. Each candidate was evaluated by quickly prototyping a subset of the RiboViz workflow, and Nextflow was chosen. The selection process took 10 person-days, a small cost for the assurance that Nextflow satisfied the authors’ requirements. The use of prototyping can offer a low-cost way of making a more informed selection of software to use within projects, rather than relying solely upon reviews and recommendations by others.

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Seven quick tips for analysis scripts in neuroimaging

Cited by 15 publications

References 27 publications

Effect of long-term paired associative stimulation on the modulation of cortical sensorimotor oscillations after spinal cord injury

Effect of long-term paired associative stimulation on the modulation of cortical sensorimotor oscillations after spinal cord injury

Open and reproducible neuroimaging: from study inception to publication

Using prototyping to choose a bioinformatics workflow management system

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