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<title>Macaque Neurodevelopment MRI Dataset — Roadmap</title>
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<header>
<h1>UNC–Wisconsin Rhesus Macaque Neurodevelopment MRI — Roadmap</h1>
<p>Concise plan to build an info page, organize scans, and surface processing pipelines and outputs for structural (T1/T2) and diffusion MRI.</p>
<div>
<span class="tag">sMRI</span>
<span class="tag">DTI</span>
<span class="tag">NRRD</span>
<span class="tag">Atlas-aligned</span>
<span class="tag">DTIPrep</span>
</div>
</header>
<section class="cards" aria-label="At a glance">
<div class="card">
<h2>At a Glance</h2>
<ul>
<li>Longitudinal macaque brain MRI spanning early postnatal to ~3 years.</li>
<li>Each scan includes structural (T1/T2) and diffusion MRI.</li>
<li>T1/T2 available in original scanner space and rigid atlas space (NRRD).</li>
<li>Diffusion provided as raw DWIs plus preprocessed outputs and tensor-derived maps.</li>
</ul>
</div>
<div class="card">
<h2>Key Resources</h2>
<ul>
<li><a href="https://data.kitware.com/#collection/54b582c38d777f4362aa9cb3" target="_blank" rel="noreferrer noopener">Data collection (Kitware)</a></li>
<li><a href="https://www.nitrc.org/projects/uncuw_macdevmri" target="_blank" rel="noreferrer noopener">Project page (NITRC)</a></li>
<li>Young et al., 2017, Frontiers in Neuroscience</li>
</ul>
</div>
</section>
<section>
<h2>Roadmap Phases</h2>
<div class="phase card">
<h3>Phase 1 — Info Page</h3>
<ul>
<li>Example slices at representative ages (e.g., ~8 months, ~14 months).</li>
<li>Tractography volume examples without subject/session identifiers.</li>
<li>Processing flowcharts:
<ul>
<li><strong>sMRI</strong>: field correction → atlas alignment → skull stripping.</li>
<li><strong>DTI</strong>: artifact correction (DTIPrep) → tensor estimation → skull stripping.</li>
</ul>
</li>
</ul>
</div>
<div class="phase card">
<h3>Phase 2 — Data Organization</h3>
<ul>
<li>Parse subject list with scan timepoints.</li>
<li>Subject directories → timepoint directories → modality folders (sMRI, DTI).</li>
<li><strong>sMRI</strong>:
<ul>
<li>Original data subfolder.</li>
<li>Atlas-registered subfolder with manual and auto brain masks.</li>
<li>Formats: NRRD.</li>
</ul>
</li>
<li><strong>DTI</strong>:
<ul>
<li><em>ORIG</em>: raw diffusion-weighted images.</li>
<li><em>MASKMANUAL</em>: manual mask folder (may be empty initially).</li>
<li><em>AUTOQC</em>: baseline, DTI_FA, DTI_MD, iDWI (auto QC products).</li>
<li><em>PROCESSED</em>: B0, DTI, FA, iDWI, MD (tensor-derived outputs).</li>
</ul>
</li>
</ul>
</div>
<div class="phase card">
<h3>Phase 3 — Surfacing Outputs</h3>
<ul>
<li>Gallery for key modalities (T1, T2, FA, MD, iDWI, B0).</li>
<li>Download pointers for original and atlas-registered sMRI (NRRD).</li>
<li>Overview of DTI preprocessing (DTIPrep) and tensor estimation.</li>
<li>Brain mask availability: manual and auto (sMRI).</li>
</ul>
</div>
<div class="phase card">
<h3>Phase 4 — Quality & Provenance</h3>
<ul>
<li>Summarize AUTOQC outputs and how to interpret them.</li>
<li>Document minimal provenance for each product (tool, parameters, version).</li>
<li>Link to primary resources and canonical publication for citation.</li>
</ul>
</div>
</section>
<section>
<h2>Directory Schema</h2>
<div class="card">
<pre>subject_list.txt # subject IDs and scan times
sub-XX/
[timepoint]/
sMRI/
ORIGINAL/
REG2ATLAS/
reg2atlas/ # transforms and aligned volumes
masks/
manual/
auto/
DTI/
ORIG/ # raw DWIs
MASKMANUAL/ # manual masks (may be empty)
AUTOQC/ # baseline, DTI_FA, DTI_MD, iDWI
PROCESSED/ # B0, DTI, FA, iDWI, MD
</pre>
</div>
</section>
<section>
<h2>Pipelines</h2>
<div class="grid-2">
<div class="card">
<h3>sMRI</h3>
<ul>
<li>Field inhomogeneity correction.</li>
<li>Rigid alignment to common atlas space.</li>
<li>Skull stripping (manual and automated masks).</li>
<li>Deliverables: original and atlas-registered T1/T2 (NRRD), masks.</li>
</ul>
</div>
<div class="card">
<h3>DTI</h3>
<ul>
<li>Artifact/motion correction via DTIPrep.</li>
<li>Tensor estimation.</li>
<li>Skull stripping.</li>
<li>Deliverables: raw DWIs, QC outputs, tensor maps (FA, MD, iDWI, B0).</li>
</ul>
</div>
</div>
</section>
<section>
<h2>Action Items</h2>
<div class="cards">
<div class="card">
<h3>Info Page Content</h3>
<ul>
<li>Curate age-based slice examples (~8m, ~14m).</li>
<li>Render tractography volume snapshots (de-identified).</li>
<li>Publish pipeline flowcharts (sMRI, DTI).</li>
</ul>
</div>
<div class="card">
<h3>Data Wiring</h3>
<ul>
<li>Load subject/timepoint table from <code>subject_list.txt</code>.</li>
<li>Map directory structure to UI routes.</li>
<li>Validate presence of expected modalities per timepoint.</li>
</ul>
</div>
<div class="card">
<h3>QC & Provenance</h3>
<ul>
<li>Summarize AUTOQC metrics and definitions.</li>
<li>Record tool versions and key parameters (DTIPrep, registration).</li>
<li>Provide citation and dataset attribution guidance.</li>
</ul>
</div>
</div>
</section>
<section>
<h2>Links</h2>
<div class="card">
<ul>
<li><a href="https://data.kitware.com/#collection/54b582c38d777f4362aa9cb3" target="_blank" rel="noreferrer noopener">Kitware Collection</a></li>
<li><a href="https://www.nitrc.org/projects/uncuw_macdevmri" target="_blank" rel="noreferrer noopener">NITRC Project Page</a></li>
<li>Young JT et al. (2017) Frontiers in Neuroscience.</li>
</ul>
</div>
</section>
<footer>
<p>Roadmap derived from project notes; external descriptions paraphrased. Update as assets and directories are verified.</p>
</footer>
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