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<!doctype html>
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<title>Data Processing Pipeline · PBS & DBIC Shared Resources</title>
<meta name="description" content="From scanner console to connectome — the standardized DBIC data pipeline: Orthanc archiving, DartFS storage, BIDS/DataLad conversion, fMRIPrep/qsiprep preprocessing, MRIQC quality control, and CANlab advanced analysis." />
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<nav class="breadcrumb" aria-label="Breadcrumb"><a href="index.html">Home</a> / <a href="mri.html">fMRI</a> / Data Pipeline</nav>
<span class="kicker">Dartmouth Brain Imaging Center</span>
<h1>From scanner console to connectome</h1>
<p class="lede">A standardized, reproducible data pipeline carries every study from the raw DICOMs on the Siemens console through archiving, BIDS conversion, preprocessing, and quality control — all the way to multivariate brain signatures and whole-brain connectomes.</p>
<span class="maintainer">Operated by DBIC & Dartmouth Research Computing · Standardized for all studies</span>
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</section>
<!-- ============ OVERVIEW SPLIT ============ -->
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<span class="eyebrow">The pipeline</span>
<h2>A single, standardized path</h2>
<p class="prose" style="color:var(--text-soft)">This pipeline is part of the DBIC fMRI workflow — the automated processing path for data collected on the <a href="mri.html">3T fMRI scanner</a>.</p>
<p class="prose" style="color:var(--text-soft)">Every scan follows the same route, so results are comparable and reproducible across studies. Data flows automatically from the scanner into managed archives and shared storage, is converted into community-standard formats, and is then preprocessed and quality-checked with well-established, openly available tools — before any lab-specific analysis begins.</p>
<ul class="spec-list" style="margin-top:1.5rem;">
<li><strong>Archiving:</strong> DICOMs pass through Orthanc for integrity checks and a temporary copy</li>
<li><strong>Storage:</strong> scans land on DartFS and appear immediately after acquisition</li>
<li><strong>Standardization:</strong> BIDS layout with DataLad versioning and sharing</li>
<li><strong>Reproducibility:</strong> containerized preprocessing that interoperates with 50+ BIDS apps</li>
</ul>
</div>
<div class="split-media" data-reveal data-reveal-delay="1">
<figure>
<img src="images/diagram-dbic-pipeline.png" alt="DBIC data pipeline diagram: DataLad/BIDS to fMRIPrep, qsiprep and MRTrix, to quality control, to brain signatures and connectomes" />
<figcaption>The DBIC pipeline: organized BIDS/DataLad datasets feed fMRIPrep, qsiprep and MRTrix, then quality control, and finally multivariate signatures and atlas-based connectomes.</figcaption>
</figure>
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</section>
<!-- ============ ACQUISITION → STORAGE ============ -->
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<span class="eyebrow" data-reveal>Stage 1 · Acquisition to storage</span>
<h2 data-reveal data-reveal-delay="1">From the console to DartFS</h2>
<p class="lede" data-reveal data-reveal-delay="2">The moment images reconstruct on the scanner, they begin an automated journey into safe, backed-up storage — no manual transfers required.</p>
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<div class="feature-grid">
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<div class="icon" aria-hidden="true">🖥️</div>
<h4>Siemens console</h4>
<p>Reconstructed DICOM images are pushed directly from the scanner console as each series completes.</p>
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<div class="feature" data-reveal data-reveal-delay="1">
<div class="icon" aria-hidden="true">🗄️</div>
<h4>Orthanc archive</h4>
<p>DICOMs pass through an Orthanc server that runs integrity checks and holds a temporary working copy.</p>
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<div class="feature" data-reveal data-reveal-delay="2">
<div class="icon" aria-hidden="true">💾</div>
<h4>DartFS storage</h4>
<p>Scans appear on the DartFS network file system immediately, with group permissions set nightly for the registered study.</p>
</div>
</div>
<div class="callout" style="margin-top:2rem;" data-reveal><strong>Immediate availability:</strong> because data lands on DartFS as it is acquired, researchers can begin inspecting and organizing a session without waiting for the scan to finish.</div>
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<!-- ============ BIDS + DATALAD SPLIT ============ -->
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<figure>
<img src="images/diagram-dbic-pipeline.png" alt="Pipeline diagram highlighting BIDS conversion and DataLad-versioned datasets" />
<figcaption>Raw DICOMs become BIDS-organized, DataLad-versioned datasets that downstream tools can read directly.</figcaption>
</figure>
</div>
<div data-reveal data-reveal-delay="1">
<span class="eyebrow">Stage 2 · Organization</span>
<h2>BIDS conversion & DataLad versioning</h2>
<p class="prose" style="color:var(--text-soft)">Data is converted into the Brain Imaging Data Structure (BIDS) using the ReproIn naming convention, producing NIfTI images alongside JSON sidecars that carry the acquisition metadata. Datasets are tracked with DataLad for transparent versioning and sharing, and a BIDS validation step flags missing, corrupt, or metadata-related errors before analysis proceeds.</p>
<ul class="spec-list" style="margin-top:1.5rem;">
<li><strong>Convention:</strong> ReproIn — consistent, self-documenting BIDS naming</li>
<li><strong>Formats:</strong> NIfTI images with paired JSON metadata sidecars</li>
<li><strong>Versioning:</strong> DataLad for reproducible tracking and sharing</li>
<li><strong>Validation:</strong> automatic checks for missing, corrupt, or metadata errors</li>
<li><strong>Interoperability:</strong> works with more than 50 community BIDS apps</li>
</ul>
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</div>
</div>
</section>
<!-- ============ PREPROCESSING FEATURE-GRID ============ -->
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<div class="container">
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<span class="eyebrow" data-reveal>Stage 3 · Preprocessing</span>
<h2 data-reveal data-reveal-delay="1">Standardized, containerized preprocessing</h2>
<p class="lede" data-reveal data-reveal-delay="2">A suite of established, openly available tools turns organized data into analysis-ready derivatives — consistently, across every modality.</p>
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<div class="feature-grid">
<div class="feature" data-reveal>
<div class="icon" aria-hidden="true">⚡</div>
<h4>fMRIPrep</h4>
<p>Realignment, coregistration, and MNI normalization, with motion and outlier derivatives generated for functional data.</p>
</div>
<div class="feature" data-reveal data-reveal-delay="1">
<div class="icon" aria-hidden="true">🧠</div>
<h4>FreeSurfer surfaces</h4>
<p>Cortical surface reconstruction with cortical thickness and volume estimates for anatomical analysis.</p>
</div>
<div class="feature" data-reveal data-reveal-delay="2">
<div class="icon" aria-hidden="true">🌐</div>
<h4>qsiprep + MRTrix</h4>
<p>Diffusion preprocessing and modeling for tractography and structural connectivity.</p>
</div>
<div class="feature" data-reveal>
<div class="icon" aria-hidden="true">📐</div>
<h4>SPM VBM</h4>
<p>Voxel-based morphometry for whole-brain analysis of gray- and white-matter structure.</p>
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<div class="feature" data-reveal data-reveal-delay="1">
<div class="icon" aria-hidden="true">🩸</div>
<h4>FSL</h4>
<p>DTI and arterial spin labeling (ASL) processing for diffusion and perfusion measures.</p>
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<div class="feature" data-reveal data-reveal-delay="2">
<div class="icon" aria-hidden="true">🧩</div>
<h4>Analysis-ready derivatives</h4>
<p>Outputs in standard spaces with confound and quality metrics, ready to plug into downstream BIDS apps.</p>
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<!-- ============ QUALITY CONTROL SPLIT ============ -->
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<span class="eyebrow">Stage 4 · Quality control</span>
<h2>Automated QC reports</h2>
<p class="prose" style="color:var(--text-soft)">Before data reaches analysis, MRIQC and cat12 generate quality-control reports for each dataset. These summarize image quality, evaluate coregistration, surface possible artifacts, and provide quantitative metrics — giving researchers an objective basis for including or excluding scans.</p>
<ul class="spec-list" style="margin-top:1.5rem;">
<li><strong>Image quality:</strong> per-scan metrics from MRIQC</li>
<li><strong>Coregistration:</strong> visual and quantitative alignment checks</li>
<li><strong>Artifacts:</strong> flags for common acquisition and motion issues</li>
<li><strong>Quantitative metrics:</strong> cat12 reports for anatomical data</li>
</ul>
</div>
<div class="split-media" data-reveal data-reveal-delay="1">
<figure>
<img src="images/diagram-dbic-pipeline.png" alt="Pipeline diagram highlighting the quality-control stage" />
<figcaption>QC reports sit between preprocessing and analysis, so only well-characterized data moves forward.</figcaption>
</figure>
</div>
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</section>
<!-- ============ ADVANCED ANALYSIS ============ -->
<section class="section section-dark reveal-bg">
<div class="container">
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<span class="eyebrow" data-reveal>Stage 5 · Advanced analysis</span>
<h2 data-reveal data-reveal-delay="1">Signatures & connectomes</h2>
<p class="lede" data-reveal data-reveal-delay="2">With clean, standardized derivatives in hand, studies move to multivariate and network-level analysis using CANlab tools developed at Dartmouth.</p>
</div>
<div class="feature-grid">
<div class="feature" data-reveal>
<div class="icon" aria-hidden="true">🔬</div>
<h4>Multivariate signatures</h4>
<p>Whole-brain multivariate patterns that serve as sensitive, interpretable brain signatures of mental states.</p>
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<h4>Atlas-based connectomes</h4>
<p>Region-to-region connectivity built on standard atlases for network-level analysis.</p>
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<div class="feature" data-reveal data-reveal-delay="2">
<div class="icon" aria-hidden="true">🎚️</div>
<h4>Confound adjustment</h4>
<p>Connectivity estimates adjusted for motion, CSF signal, and outliers using CANlab tools.</p>
</div>
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<!-- ============ ACCESS / CONTACT ============ -->
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<span class="eyebrow" data-reveal>Access & support</span>
<h2 data-reveal data-reveal-delay="1">Getting your study on the pipeline</h2>
<p class="prose" data-reveal data-reveal-delay="2" style="color:var(--text-soft)">The pipeline is standardized for all DBIC studies and operated jointly by the DBIC and Dartmouth Research Computing. Once a study is registered, its data flows automatically from the scanner into DartFS and can be converted, preprocessed, and quality-checked using the shared, reproducible tooling described above. Research Computing supports setup, access, and troubleshooting.</p>
<div class="callout" data-reveal><strong>Contact:</strong> Dartmouth Research Computing · <a href="mailto:research.computing@dartmouth.edu">research.computing@dartmouth.edu</a></div>
<div style="margin-top:1.6rem;" data-reveal>
<a class="btn btn-primary btn-arrow" href="mailto:research.computing@dartmouth.edu">Ask about the pipeline</a>
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<span>© <span data-year>2026</span> Dartmouth Brain Imaging Center · Department of Psychological and Brain Sciences</span>
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