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| <title>Macaque Neurodevelopment MRI Dataset — Roadmap</title> | |
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| <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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