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<h2 id="why-use-bids-">1. Why Use BIDS?</h2>
<p>Brain Imaging Data Structure (BIDS) is a standard for organizing, annotating, and describing data neuroimaging and behavioral data. BIDS offers several advantages:</p>
<ul>
<li><strong>Standardization</strong>: Ensures data consistency across studies.</li>
<li><strong>Interoperability</strong>: Facilitates data sharing and collaboration.</li>
<li><strong>Tool Compatibility</strong>: Compatible with various neuroimaging analysis tools.</li>
<li><strong>Reproducibility</strong>: Promotes reproducible research practices.</li>
</ul>
<p>For a detailed overview, you can visit the <a href="https://bids.neuroimaging.io/">official BIDS website</a>.</p>
<h2 id="key-features-of-bids">2. Key Features of BIDS</h2>
<ol>
<li><strong>File Naming and Organization</strong>: BIDS specifies a consistent naming convention and folder structure.</li>
<li><strong>Metadata</strong>: Comprehensive metadata standards to describe data acquisition parameters.</li>
<li><strong>Data Types</strong>: Supports various data types, including MRI, MEG, EEG, iEEG, and more.</li>
<li><strong>Extensions</strong>: Allows for community-driven extensions to support new data types and modalities.</li>
</ol>
<h2 id="getting-started-with-bids">3. Getting Started with BIDS</h2>
<p>To start using BIDS, you can refer to the <a href="https://bids-standard.github.io/bids-starter-kit/">BIDS Starter Kit</a>. This resource provides templates, examples, and guidelines for converting your data to BIDS format.</p>
<h2 id="converting-data-to-bids-format">4. Converting Data to BIDS Format</h2>
<p>To simplify the process of converting neuroimaging data to BIDS format, various software tools known as BIDS converters have been developed. A non-exhaustive list of available BIDS converters can be found <a href="https://bids.neuroimaging.io/benefits">here</a>.</p>
<p>Many of the original and most popular BIDS converters, such as <strong>HeuDiConv</strong> and <strong>Dcm2Bids</strong>, require users to create custom code to specify the mapping between their imaging data and resulting BIDS output. However, newer tools have been developed to minimize or eliminate the need for coding by making educated guesses about the data's identity and suggesting the appropriate BIDS information and structure. For example, <strong>BIDScoin</strong> offers a graphical user interface (GUI), making it user-friendly, while <strong>ezBIDS</strong> takes a web-based approach. These newer tools are particularly useful for researchers who are less familiar with BIDS or not well-versed in the syntax and structure of the older converters. While the older BIDS converters provide more flexibility, the newer tools are designed to be more accessible and easier to use.</p>
<h2 id="tools-for-working-with-bids-data">5. Tools for Working with BIDS Data</h2>
<ul>
<li><strong>nipopy:</strong> Lightweight neuroimaging workflow manager to help with DICOM to BIDS conversion and running BIDS apps</li>
<li><strong>BIDS Validator</strong>: A tool to ensure your dataset conforms to BIDS specifications.</li>
<li><strong>pyBIDS</strong>: A Python library to query and manipulate BIDS datasets. Learn more in the <a href="https://bids-standard.github.io/pybids/introduction.html#what-is-bids-and-why-should-you-use-it">pyBIDS documentation</a>.
ss this tool, go to the <a href="https://bids-standard.github.io/bids-validator/">BIDS Validator webpage</a></li>
<li><strong>BIDS Apps</strong>: Once you have converted data BIDS, you are ready to begin using BIDS apps, which are a collection of neuroimaging data analysis pipelines that accept BIDS-formatted data as input, such as MRIQC and fMRIPrep. Learn more in the <a href="https://bids-apps.neuroimaging.io/">BIDS App page</a></li>
</ul>
<h2 id="detailed-guides-and-tutorials">6. Detailed Guides and Tutorials</h2>
<ul>
<li><strong>Andy's Brain Book BIDS Overview</strong>: An introductory guide to BIDS, available on <a href="https://andysbrainbook.readthedocs.io/en/latest/OpenScience/OS/BIDS_Overview.html">Andy's Brain Book</a>.</li>
<li><strong>RPubs Tutorial</strong>: A comprehensive guide on BIDS with subsequent tutorials on using fMRIPrep and MRIQC, available on <a href="https://rpubs.com/sarenseeley/bids-fmriprep-mriqc">RPubs</a>.</li>
<li><strong>OSF Guide</strong>: A step-by-step guide to creating BIDS datasets, available on the <a href="https://osf.io/dcbfj">Open Science Framework</a>.</li>
</ul>
<h2 id="literature-and-documentation">7. Literature and Documentation</h2>
<li><strong>A detailed description of the development of BIDS and benefits, can be found in the foundational BIDS <a href="https://www.nature.com/articles/sdata201644">paper published in Nature</a>.</p>
<li><strong>A description of how to build containerized apps supporting BIDS inputs can be found in the <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005209">paper published in PLOS Computational Biology</a>.</p>
<li><strong>For the official specification and in-depth documentation, refer to the <a href="https://bids-specification.readthedocs.io/en/stable/">BIDS Specification</a>.</p>
<h2 id="conclusion">8. Conclusion</h2>
<p>BIDS is a powerful standard that enhances the organization, sharing, and analysis of neuroimaging data. By adopting BIDS, researchers can improve the reproducibility of their studies and facilitate broader collaboration within the neuroscience community.</p>
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