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Rationale

The goal of this standard is to have a uniform interface for software tools for musculoskeletal image processing and analysis.

Ideally, each tool will have a command-line interface with the following syntax:

musculoskeletal_tool <patient_folder>

Where the patient_folder is the location of the root folder containing all the acquired data for a patient, divided into subfolders according to the MIDS extension of the BIDS standard, and as described below. The musculoskeletal tools will also output data in the correct format in the same folder structure. **NOTE: ** One important difference between ORMIR-MIDS and BIDS is that all MR-related outputs are prefixed by ‘mr-‘ in ORMIR-MIDS (e.g. mr-anat, mr-quant, etc.). Please take this into consideration when handling ORMIR-MIDS-derived data.

General guidelines

Guidelines for specific scan types

Implemented or partially implemented

Imaging method/sequence NIfTI structure Filename suffix Folder JSON required fields
Computed tomography 3D (x,y,z) N/A ct
  • XRayEnergy in kVp
  • XRayExposure in mAs
Computed/ plain radiography 2D (x,y) N/A cr
  • ExposureTime in ms
  • X-RayTubeCurrent in mA
MRI: Multi-echo gradient echo 4D (x,y,z,echo) megre mr-anat
  • EchoTime (array) in ms
  • WaterFatShift in pixels
  • MagneticFieldStrength
  • [proposed] ReadoutMode: Monopolar/Bipolar
  • [proposed] PrecessionDirection: Counter-/Clockwise
MRI: Multi-echo spin echo 4D (x,y,z,echo) mese mr-anat
  • EchoTime (array) in ms
  • RefocusingFlipAngle in degrees
  • [optional] ExcitationProfile and RefocusingProfile (arrays) providing the slice profiles in degrees
MRI: T1w / T1w-FS / T2w / T2w-FS 3D (x,y,z) t1w / t1w-fs / t2w / t2w-fs mr-anat
MRI: Quantitative T1 / T2 / wT2 3D (x,y,z) t1 / t2 / wt2 mr-quant

Not implemented / Proposed

Imaging method/sequence NIfTI structure Filename suffix Folder JSON required fields
High-resolution peripheral quantitative computed tomography 3D (x,y,z) N/A hrpqct
  • XRayEnergy in kVp
  • XRayExposure in mAs
MRI: Phase contrast 4D (x,y,z,t) + suffix per venc direction pc_mag / pc_ph_1 / pc_ph_2 / pc_ph_3 mr-flow?? The velocity information is stored as phase data scaled between -π and +π
  • Venc in cm/s
  • EncodingDirection (3D vector) for each phase volume, indicating the direction of the positive velocity encoding for that volume. TBD: patient coordinate system or image coordinate system
MRI: DESS 4D (x,y,z,echo) dess mr-anat
  • EchoTime (array) in ms
MRI: Diffusion 4D (x,y,z,direction) diff mr-diff
  • MixingTime in ms
  • EncodingDirection (array of 3D vectors). The norm of the vector is the b-value. The normalized vector indicates the direction of the diffusion gradient in patient coordinates
Segmentation labels
  • 3D (x,y,z) with integer values, 0---N, each corresponding to a different label
  • 4D (x,y,z,label) stack of binary (0/1) values, each dimension corresponding to a label
seg?? seg??
  • Labels (array of strings). List of the labels represented in the masks. The first value in the list corresponds to either a gray level of 0 or to the 1st volume in the fourth dimension. E.g. ["Background", "SOL", "VM", "VL"]
  • Note: the string representation of the labels must follow a standardized format. While it is possible that the same anatomical structure is represented by different labels (e.g. SOL or Soleus), the labels must be known. This allows flexibility in the implementation of segmentation tools, while keeping easy interoperability because all values are easily convertible. A list of standardized labels is visible here. Please contact Francesco Santini if you would like to add your own definitions