ORMIR-MIDS AS A STANDARD SPECIFICATION

ORMIR-MIDS AS A STANDARD SPECIFICATION#

The ORMIR-MIDS specifications are a simple and intuitive way to organize MSK imaging data. They are an extension of the specifications of the Brain Imaging Data Structure (BIDS) and the Medical Imaging Data Structure (MIDS)

In this page, you will find:
1. Structure and naming of folders and files
2. Supported imaging modalities

Structure and naming of folders and files#

Folder structure#

The folder structure is hierarchical and composed of 4 levels of nested folders:
Dataset → Subject → Session → Imaging Method

ORMIR-MIDS folder structure

  • Dataset: root (or parent) folder containing all the MSK data (E.g., Dataset_organized)

  • Subject: folder(s) containing all the data about a single subject (E.g., sub-01 for the first subject)

  • Session: folder(s) containing the data of an acquisition session at a specific time point(E.g., ses-01 for baseline acquisitions)

  • Imaging Method: folder(s) containing the data of a specific acquisition. (E.g., mr-anat for anatomical MR images). You can find the currently supported imaging methods in this table

Filesystem structure#

Within each folder or subfolder, there are specific files:

ORMIR-MIDS file system structure

  • Participants’ information: definition under construction!

  • Scans’ information: definition under construction!

  • Session information: definition under construction!

  • Image volume: 3D image

  • Image information: Header of the dicom images in .json format

Folder naming#

  • Folders have precise names:

ORMIR-MIDS folder nomenclature

  • Folder names referring to subjects and sessions are composed of two parts:

    1. sub or ses, indicating subject (blue in the figure above) or session (purple in the figure above)

    2. <ID> of the subject or of the session (e.g., 01)

    Note: The two parts are separated by dash (-)

  • Folder names referring to image modalities (yellow in the figure above) can have various names, such as mr-anat, ct, etc. For a list of the available names, see the second column (called Folder name) in the table below

File naming#

  • Files have precise names:

ORMIR-MIDS file nomenclature

  • Each file name is composed of three parts, each of them containing information about:

    1. Subject, such as sub-01 (blue in the figure above)

    2. Session, such as ses-01 (purple in the figure above)

    3. File content, such as scans, metadata, etc. (green in the figure above). For the images, you can find the currently supported file types in the table below

    Note: The three parts are separated by underscore (_)

Supported imaging modalities#

In the following table, you will find the image data types that are currently implemented or under development in ORMIR-MIDS. The table columns specify:

  • Imaging method: the image acquisition method, such as computed tomography, MR imaging, etc.

  • Folder name: name of the output folder containing the images (e.g., mr-anat, ct, etc.). See the folder naming specifications for more details

  • File name suffix: suffix of the file name of the image volume (e.g., mese, megre, etc.). See the file naming specifications for more details

  • Image volume: dimension (2D, 3D, or 4D) and directions (x, y, z, echo) of the obtained image volume (i.e., nii.gz files)

  • JSON fields: information that the dicom header must have to be able to transform the data into the ORMIR-MIDS structure

Imaging method

Folder name

File name suffix

Image volume

JSON fields

Computed tomography

ct

N/A

3D (x,y,z)

XRayEnergy in kVp
XRayExposure in mAs

Computed / plain radiography

cr

N/A

2D (x,y)

ExposureTime in ms
X-RayTubeCurrent in mA

MRI: Multi-echo gradient echo

mr-anat

megre

4D (x,y,z,echo)

EchoTime (array) in ms
WaterFatShift in pixels
MagneticFieldStrength
proposed: ReadoutMode: Monopolar/Bipolar
proposed: PrecessionDirection: Counter-/Clockwise

MRI: Multi-echo spin echo

mr-anat

mese

4D (x,y,z,echo)

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

mr-anat

t1w / t1w-fs / t2w / t2w-fs

3D (x,y,z)

MRI: Quantitative T1 / T2 / wT2

mr-quant

t1 / t2 / wt2

3D (x,y,z)

Note: We are also working on conversions for:

  • More imaging modalities, such as HR-pQCT, MRI Phase contrast, MRI DESS, MRI Diffusion

  • Derived data, such as segmentation labels

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