Manuals and scripts

All files are in the QMRITools GitHub repository.

Manuals

• Muscle-BIDS manual The full manual for the Muscle-BIDS pipeline, from DICOM conversion, via the config file, processing, segmentation and tractography to the per-muscle analysis. Also available as a pdf. A short introduction is given here.
• Processing flowchart Overview of the Muscle-BIDS processing steps (notebook).
• All functions A list of all functions with their documentation, also as notebook. The same documentation is available as online guide pages.

Example Muscle-BIDS configurations

Example config files for different studies. Use them as a starting point for your own project.

• config.json: the default configuration
• boch_config.json
• motion_config.json
• motor_config.json
• twitch_config.json

Scripts

The scripts run from the command line with the free Wolfram Engine and do not need Mathematica. A step by step manual is given here.

• Install_QMRITools.wls Installs QMRITools (latest or a specific release) for the Wolfram Engine.
• Segment_Nii.wls Segments a NIfTI file with the trained muscle segmentation networks. Example data is in the test data folder.
• segmentGUI.nb A notebook with a graphical interface for segmentation within Mathematica.

Demonstration notebooks and data

• Demonstrations.nb with demonstrations of most toolboxes, see here. After installation open it with OpenDemonstrationNotebook[].
• Demo_UNet.nb shows how to build and train a segmentation network.
• DemoData: the data sets used in the demonstrations (DemoData.zip).

Gradient design

The interactive diffusion gradient design tool is also available as notebook.