ormir-mids 0.1.8

Library for standardized data input/output for musculoskeletal imaging, based on BIDS

ORMIR-MIDS

ORMIR-MIDS is both a specification and a package to standardiza Medical Image Data Structure (MIDS) for Open and Reproducible Musculoskeletal Imaging Research (ORMIR). ORMIR-MIDS is based on the BIDS data structure for brain imaging data and on muscle-bids for muscle MR imaging data.

Main contributors

• Donnie Cameron
• Francesco Santini
• Jukka Hirvasniemi
• Maria Monzon Ronda
• Serena Bonaretti
• Gianluca Iori
• Francesco Chiumento
• Simone Poncioni
• Michelle Alejandra Espinoza Hernandez
• Youngjun Lee

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Installation

To install ORMIR-MIDS via pip use the following command in your terminal:

pip install ormir-mids

Note: The installation of ORMIR-MIDS requires the following dependencies

Development installation

If you want to contribute to ORMIR-MIDS, start by cloning the repository:

git clone https://github.com/ormir-mids/ormir-mids.git

Then, install via conda (in a separate virtual environment):

conda env create -n ormir-mids
conda activate ormir-mids

or via pip:

cd ormir-mids
pip install .
pip install --upgrade nibabel # the default nibabel has bugs

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Usage

To use ORMIR-MIDS in your code, import it as:

import ormir_mids

To run ORMIR-MIDS from terminal, the command is:

dcm2omids -anonymize <pseudo_name> -recursive <input_dir> <output_dir>

Note: ormir-mids can be used for two purposes:

1. To convert DICOM data to the ORMIR-MIDS format
2. As a Python module to find, load, and interrogate ORMIR-MIDS-format data. For further clarification, see the demo notebook

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Documentation and tutorials

To learn how to use ORMIR-MIDS:

• Read the ORMIR-MIDS website for background information about the standard and the package
• Run the demo notebook either locally or on )

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How to contribute

To contribute to ORMIR-MIDS:

• Install ORMIR-MIDS for development (see above)
• Create a branch and make your changes and/or additions. If you want to coordinate the development with the main maintainers, write to Donnie Cameron or Francesco Santini
• Commit your changes and send a pull request
• To write a new converter class, refer to the Example Converter Class

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API documentation

You can find the API documentation of ORMIR-MIDS on Read the Docs

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Citation

When using ORMIR-MIDS, please cite the following abstract (paper coming in the next months!):

S. Bonaretti, M. A. Espinosa Hernandez, F. Chiumento, Y. Founas, M. Froeling, J. Hirvasniemi, G. Iori, Y. Lee, S. Matuschik, M. Monzon, F. Santini, D. Cameron. ORMIR-MIDS:An open standard for curating and sharing musculoskeletal imaging data. 24th International Workshop on Quantitative Musculoskeletal Imaging (QMSKI) The Barossa Valley, South Australia. November 3-8, 2024.

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Licence

ORMIR-MIDS is released under Apache 2.0

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Legal aspects

This code is freely available only for research purposes. The software has not been certified as a medical device and, therefore, must not be used for diagnostic purposes.

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Acknowledgement

The development of ORMIR-MIDS specification and package started during the 2nd ORMIR workshop Sharing and Curating Open Data in Musculoskeletal Imaging Research and is currently ongoing.

ORMIR-MIDS is an extension of muscle-BIDS, which was partly developed during the 1st ORMIR workshop Building the Jupyter Community in Musculoskeletal Imaging Research.

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ReadMe file created using the template of the ORMIR community (version 1.0, 2023)