UNC–Wisconsin Rhesus Macaque Neurodevelopment MRI — Roadmap

Concise plan to build an info page, organize scans, and surface processing pipelines and outputs for structural (T1/T2) and diffusion MRI.

sMRI DTI NRRD Atlas-aligned DTIPrep

At a Glance

  • Longitudinal macaque brain MRI spanning early postnatal to ~3 years.
  • Each scan includes structural (T1/T2) and diffusion MRI.
  • T1/T2 available in original scanner space and rigid atlas space (NRRD).
  • Diffusion provided as raw DWIs plus preprocessed outputs and tensor-derived maps.

Key Resources

Roadmap Phases

Phase 1 — Info Page

  • Example slices at representative ages (e.g., ~8 months, ~14 months).
  • Tractography volume examples without subject/session identifiers.
  • Processing flowcharts:
    • sMRI: field correction → atlas alignment → skull stripping.
    • DTI: artifact correction (DTIPrep) → tensor estimation → skull stripping.

Phase 2 — Data Organization

  • Parse subject list with scan timepoints.
  • Subject directories → timepoint directories → modality folders (sMRI, DTI).
  • sMRI:
    • Original data subfolder.
    • Atlas-registered subfolder with manual and auto brain masks.
    • Formats: NRRD.
  • DTI:
    • ORIG: raw diffusion-weighted images.
    • MASKMANUAL: manual mask folder (may be empty initially).
    • AUTOQC: baseline, DTI_FA, DTI_MD, iDWI (auto QC products).
    • PROCESSED: B0, DTI, FA, iDWI, MD (tensor-derived outputs).

Phase 3 — Surfacing Outputs

  • Gallery for key modalities (T1, T2, FA, MD, iDWI, B0).
  • Download pointers for original and atlas-registered sMRI (NRRD).
  • Overview of DTI preprocessing (DTIPrep) and tensor estimation.
  • Brain mask availability: manual and auto (sMRI).

Phase 4 — Quality & Provenance

  • Summarize AUTOQC outputs and how to interpret them.
  • Document minimal provenance for each product (tool, parameters, version).
  • Link to primary resources and canonical publication for citation.

Directory Schema

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

Pipelines

sMRI

  • Field inhomogeneity correction.
  • Rigid alignment to common atlas space.
  • Skull stripping (manual and automated masks).
  • Deliverables: original and atlas-registered T1/T2 (NRRD), masks.

DTI

  • Artifact/motion correction via DTIPrep.
  • Tensor estimation.
  • Skull stripping.
  • Deliverables: raw DWIs, QC outputs, tensor maps (FA, MD, iDWI, B0).

Action Items

Info Page Content

  • Curate age-based slice examples (~8m, ~14m).
  • Render tractography volume snapshots (de-identified).
  • Publish pipeline flowcharts (sMRI, DTI).

Data Wiring

  • Load subject/timepoint table from subject_list.txt.
  • Map directory structure to UI routes.
  • Validate presence of expected modalities per timepoint.

QC & Provenance

  • Summarize AUTOQC metrics and definitions.
  • Record tool versions and key parameters (DTIPrep, registration).
  • Provide citation and dataset attribution guidance.

Links