Naming conventions of files and folders

Files and folders

Muscle-BIDS file structure explained.

Within the bids standard filenames contain information label such as subject name, data type and sessions followed by a suffix containing extra information. Each label if followed by a value \<label\>-\<value\> connected by a "-". Each label is concatenated by a "\_", for example sub-PAT001_ses-001. After the last “_” any number of suffixes can follow. The data type is the first suffix, for example sub-PAT001_ses-001_dwi.nii.gz.

File Names

Next to the folder structure, the file names of a Muscle-BIDS dataset will tell a lot about what kind of file it is and what it contains. A Muscle-BIDS name contains a list of entities followed by a list of suffixes and is ended with an extension. In Muscle-BIDS filenames "-" and "_" have special meanings and can never be used outside their intended use.

  • An entity starts with a known key followed by its value (label or index) separated by an "-” and multiple entities are separated by a "_" Example: <key1>-<label>_<key2>-<index>
  • A suffix or list of suffixes comes after the entities and each suffix is separated by a "_"
    • The first suffix describes the data type and must be maintained
    • The rest of the suffixes can be ones chosen from the defined suffixes per data type or a custom one Example: <key1>-<label>_<key2>-<index>_<suf1>_<suf2>
  • The extension finalizes the file name Example: <key1>-<label>_<key2>-<index>_<suf1>_<suf2>.<ext>

Based on the Muscle-BIDS filename and its location it should be clear what data is contained within the file. Some examples are:

  • “sub-test01_ses-001_megre_b0.nii”
  • “sub-test01_ses-001_rep-flexion_dwi_dti_md.nii”
  • “sub-anonab_ses-002_stac-upper_wt2_t2.nii.gz”
  • “sub-anonab_ses-002_stac-upper_wt2_t2.json”

Folders

To prevent ambiguity most MRI acquisitions are stored in predefined folders. Muscle-BIDS-compliant software will look in these folders for their needed raw source data. The following folders have been defined in Muscle-BIDS. QMRITools uses the following subfolders to store data in the Muscle-BIDS dataset.

  • anat: Structural imaging for anatomical or diagnostic reference (e.g T1 or T2).
  • dwi: Diffusion-weighted data (e.g. DTI or IVIM).
  • dix: Dixon data.
  • quant: Relaxometry data (e.g. T1 or T2 mapping).
  • seg: Segmentation labels (e.g. manual segmentations).
  • raw: Unspecified non-BIDS files.

An example of a folder structure is shown below:

└─example/
  ├─sub-cont001/
  │ ├─ses-visit1a/
  │ │ ├─dix/
  │ │ ├─quant/
  │ │ └─raw/
  │ ├─ses-visit1b/
  │ │ ├─dix/
  │ │ ├─dwi/
  │ │ ├─quant/
  │ │ └─raw/
  │ └─ses-visit2/
  │   ├─dwi/
  │   └─raw/
  ├─sub-pat0054/
  │ ├─ses-visit1/
  │ │ ├─dwi/
  │ │ ├─quant/
  │ │ └─raw/
  │ └─ses-visit2/
  │   ├─dix/
  │   ├─dwi/
  │   └─raw/
  └─sub-test002/
    ├─ses-visit1/
    │ ├─quant/
    │ └─raw/
    └─ses-visit2/
      ├─dwi/
      ├─quant/
      └─raw/