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bids-scan

A quick one-liner tool to extract site metadata from a BIDS dataset. The resulting output can be directly used for a publication, or a website for example.

Warning

We suppose that each patient from the same site (and same modality, task) will have the same parameters.

Input

A BIDS compatible f-mri data directory.

Output

The sites parameters matrix as a csv table in the reStructured Text format.

For example for f-MRI:

f-MRI sites parameters
Site Field Strength (T) Voxel size (mm3) Matrix size Flip Angle TE (s) TR (s) Volumes Scan slices order Scan time (min)
THE_OTTAWA_HOSPITAL_CIVIC 3 3.5 64x64 70 0.03 2.11 250 sequential decreasing 8.79

Usage

bids_scan.py --data /ccna

Ignore

You can append path(s) to ignore with the --ignore parameter.

bids_scan.py --data /ccna --ignore /ccna/phenotype --ignore /ccna/sub-XXX0000/

Modality

Select which modality you are interrested in with --modality.

bids_scan.py --data /ccna --ignore /ccna/phenotype --modality func

Requirements

  • pybids 0.12.3
  • nibabel 3.2.1

pybids is the python wrapper aroung the bids dataset. nibabel get the imaging parameters (number of volumes, resolution, slice order method and scan time) directly from the NIfTI file if not correctly gathered.