OpenMSK example data
====================

This is one real knee MRI and every output OpenMSK produced for it, generated by
the same pipeline the website runs. Use it to see what a suitable input looks
like and what you get back, without uploading anything of your own.

The scan is a maintainer's own knee, published deliberately. It carries no
patient identifiers, and the files are named after this example rather than the
original.

FILES
-----
openmsk-example-knee.nrrd
openmsk-example-bundle.zip (this archive)

Segmentation:
  openmsk-example-knee_all-labels.nii.gz
  openmsk-example-knee_all-labels.nrrd
  openmsk-example-knee_subregions-labels.nii.gz
  openmsk-example-knee_subregions-labels.nrrd
Surface meshes:
  femur_cart_0_mesh.vtk
  femur_mesh.vtk
  patella_cart_0_mesh.vtk
  patella_mesh.vtk
  tibia_cart_0_mesh.vtk
  tibia_cart_1_mesh.vtk
  tibia_mesh.vtk
Cartilage thickness:
  openmsk-example-knee_results.csv
  openmsk-example-knee_results.json
Shape model + BScore:
  NSM_bone_only_recon_femur_mesh_NSM_orig.vtk
  NSM_bone_only_recon_params.json
  NSM_recon_fem_cart_mesh_NSM_orig.vtk
  NSM_recon_femur_mesh_NSM_orig.vtk
  NSM_recon_params.json
  fem_cart_mesh_NSM_orig.vtk
  femur_mesh_NSM_orig.vtk
Run settings:
  _step_log.json
  job_manifest.json

INPUT
-----
openmsk-example-knee.nrrd -- the image that produced everything else. A sagittal knee MRI
in NRRD format, 512 x 512 x 96 voxels at 0.312 x 0.313 x 1 mm. NRRD holds the voxel
data and geometry only, so it carries no DICOM metadata.

You can upload this file to openmsk.com as-is to reproduce these results.

WHERE THE NUMBERS ARE
---------------------
Two things here are not guessable from the file listing, and both cost real time
to work out:

  Cartilage thickness is stored on the BONE meshes, not the cartilage meshes.
  femur_mesh.vtk, tibia_mesh.vtk and patella_mesh.vtk each carry a per-vertex
  "thickness (mm)" array, plus a "labels" array giving the cartilage region each
  vertex belongs to. Thickness is measured outward from the bone surface, which
  is why it lives there. Colour a bone mesh by "thickness (mm)" in ParaView or
  3D Slicer and you have a thickness map. The cartilage meshes are geometry only
  and carry no point data. Region summaries are in *_results.csv / *_results.json.

  BScore is not a file. It is the "Bscore" key inside NSM_recon_params.json and
  NSM_bone_only_recon_params.json. Searching filenames for "bscore" finds
  nothing, which looks like the feature is missing -- it is not.

A NOTE ON T2
------------
This example has no T2 map, and that is expected rather than a failure.
T2 mapping requires a qDESS DICOM series, where T2 is computed from the ratio of
two echoes plus gradient spoiling parameters held in the DICOM headers. A
single-volume NRRD like this one cannot carry that information, so the pipeline
skips the step. Upload a qDESS DICOM series to get T2 maps.

REUSE
-----
Free to use for research and teaching. Not for clinical use -- see
https://openmsk.com/terms

If OpenMSK contributes to your work, please cite:

  Goyal A, Belibi F, Sahani V, Pedersen R, Vainberg Y, Williams A, Chu C,
  Haddock B, Gold G, Chaudhari A, Kogan F, Gatti A. Automating Imaging Biomarker
  Analysis for Knee Osteoarthritis Using an Open-Source MRI-Based Deep Learning
  Pipeline. medRxiv 2025. doi:10.1101/2025.02.21.25322094

Generated 2026-08-13 from OpenMSK pipeline run a196fa20-2ac4-40f3-b23f-bcd203c64723.
