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利用逼真的功能磁共振成像模拟促进开放科学:验证与应用

Facilitating open-science with realistic fMRI simulation: validation and application.

作者信息

Ellis Cameron T, Baldassano Christopher, Schapiro Anna C, Cai Ming Bo, Cohen Jonathan D

机构信息

Department of Psychology, Yale University, New Haven, CT, United States of America.

Department of Psychology, Columbia University, New York, NY, United States of America.

出版信息

PeerJ. 2020 Feb 19;8:e8564. doi: 10.7717/peerj.8564. eCollection 2020.


DOI:10.7717/peerj.8564
PMID:32117629
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7035870/
Abstract

With advances in methods for collecting and analyzing fMRI data, there is a concurrent need to understand how to reliably evaluate and optimally use these methods. Simulations of fMRI data can aid in both the evaluation of complex designs and the analysis of data. We present fmrisim, a new Python package for standardized, realistic simulation of fMRI data. This package is part of BrainIAK: a recently released open-source Python toolbox for advanced neuroimaging analyses. We describe how to use fmrisim to extract noise properties from real fMRI data and then create a synthetic dataset with matched noise properties and a user-specified signal. We validate the noise generated by fmrisim to show that it can approximate the noise properties of real data. We further show how fmrisim can help researchers find the optimal design in terms of power. The fmrisim package holds promise for improving the design of fMRI experiments, which may facilitate both the pre-registration of such experiments as well as the analysis of fMRI data.

摘要

随着功能磁共振成像(fMRI)数据采集和分析方法的进步,同时需要了解如何可靠地评估和最佳地使用这些方法。fMRI数据模拟有助于复杂设计的评估和数据分析。我们展示了fmrisim,这是一个用于fMRI数据标准化、逼真模拟的新Python包。这个包是BrainIAK的一部分:一个最近发布的用于高级神经成像分析的开源Python工具箱。我们描述了如何使用fmrisim从真实fMRI数据中提取噪声特性,然后创建一个具有匹配噪声特性和用户指定信号的合成数据集。我们验证了fmrisim生成的噪声,以表明它可以近似真实数据的噪声特性。我们进一步展示了fmrisim如何帮助研究人员在功效方面找到最佳设计。fmrisim包有望改进fMRI实验的设计,这可能有助于此类实验的预注册以及fMRI数据的分析。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2900/7035870/1b94940a4620/peerj-08-8564-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2900/7035870/d978d781031a/peerj-08-8564-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2900/7035870/7287b616ff05/peerj-08-8564-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2900/7035870/14ff4863e869/peerj-08-8564-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2900/7035870/b16edfe908a4/peerj-08-8564-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2900/7035870/1b94940a4620/peerj-08-8564-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2900/7035870/d978d781031a/peerj-08-8564-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2900/7035870/7287b616ff05/peerj-08-8564-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2900/7035870/14ff4863e869/peerj-08-8564-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2900/7035870/b16edfe908a4/peerj-08-8564-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2900/7035870/1b94940a4620/peerj-08-8564-g005.jpg

相似文献

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[2]
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引用本文的文献

[1]
SNAKE: A modular realistic fMRI data simulator from the space-time domain to k-space and back.

Imaging Neurosci (Camb). 2025-9-2

[2]
Emotions in the Brain Are Dynamic and Contextually Dependent: Using Music to Measure Affective Transitions.

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[3]
Multi-Metric Approach for the Comparison of Denoising Techniques for Resting-State fMRI.

Hum Brain Mapp. 2025-5

[4]
Deconstructing the Mapper algorithm to extract richer topological and temporal features from functional neuroimaging data.

Netw Neurosci. 2024-12-10

[5]
Computational Language Modeling and the Promise of In Silico Experimentation.

Neurobiol Lang (Camb). 2024-4-1

[6]
Static and dynamic fMRI-derived functional connectomes represent largely similar information.

Netw Neurosci. 2023-12-22

[7]
Deconstructing the Mapper algorithm to extract richer topological and temporal features from functional neuroimaging data.

bioRxiv. 2023-10-19

[8]
Optimizing cognitive neuroscience experiments for separating event- related fMRI BOLD responses in non-randomized alternating designs.

Front Neuroimaging. 2023-4-17

[9]
Static and dynamic functional connectomes represent largely similar information.

bioRxiv. 2023-5-16

[10]
BrainIAK: The Brain Imaging Analysis Kit.

Apert Neuro. 2021

本文引用的文献

[1]
A manifesto for reproducible science.

Nat Hum Behav. 2017-1-10

[2]
BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis.

PLoS Comput Biol. 2020-1-15

[3]
Feasibility of topological data analysis for event-related fMRI.

Netw Neurosci. 2019-7-1

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Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias.

PLoS Comput Biol. 2019-5-24

[5]
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Nat Methods. 2018-12-10

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Nat Neurosci. 2017-2-23

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Nat Commun. 2016-7-18

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