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The goal of this standard is to have a uniform interface for software tools for muscle imaging.

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

muscle_tool <patient_folder>

Where the patient_folder is the location of the root folder containing all the acquired data for a patient, divided in subfolders according to the BIDS standard and as described below. The muscle tools will also output data in the correct format in the same folder structure.

General guidelines

Guidelines for specific scan types

Implemented or partially implemented

Multi-echo gradient echo

Multi-echo spin echo

T1w / T1w-FS / T2w / T2w-FS

Quantitative T1 / T2 / wT2

Not implemented / Proposed

Phase contrast


Segmentation labels