NIFTI metadata extension

Quantiphyse stores various metadata about its data sets which it would be useful to persist across loading and saving. The NIFTI format provides for this in the form of ‘header extensions’.

Each header extension is identified by a code number so software can choose to pay attention only to header extensions that it knows about. Quantiphyse has been assigned the code 42 for its header extensions.

Quantiphyse extensions will be stored as strings in YAML format for easy serialization/deserialization to Python and because YAML is already used as the basis for the batch format.

There has been suggestion that nibabel may add its own metadata as a NIFTI extension. This might enable some of the Quantiphyse metadata to be deprecated, however this is not available at present. It may also be possible to align this metadata with the BIDS standard in the future.

The following set of metadata is an initial proposal, however any widget can save its own metadata by adding a YAML-serializable object to the data sets metadata dictionary attribute. Hence this list is not exhaustive.

Generic metadata

    roi : True/False        # Whether the data set should be treated as an ROI
    regions :               # ROI regions (codes and names)
        1 : tumour
        2 : nodes
    raw-2dt : True          # Indicates that 3D data should be interpreted as 2D+time
    dps: 3                  # Suggested number of decimal places to display for values

ASL data set structure

  tis : [1.4, 1.6, ...]     # List of TIs
  plds : [2.5, 2.6, ...     # List of PLDs, alternative to TIs
  rpts : [4, 4, 4, ...]     # Repeats at each TI/PLD
  phases : [0, 45, 90, ...] # Phases in degrees for multiphase data
  nphases : 8               # Alternatively, number of evenly-spaced phases

CEST data set structure

  freq-offsets : [-300, -30, 0, 10, 20, ...] # Frequency offsets
  b0 : 9.4                                   # Field strength in T
  b1 : 0.55                                  # B1 in microT
  sat-time : 2                               # Continuous saturation time in s
  sat-mags : [1, 2, 3, 4, ...]               # Pulsed saturation magnitudes
  sat-durs : [1, 3, 2, 4, ...]               # Pulsed saturation durations in s
  sat-rpts : 1                               # Pulsed saturation repeats