PCT list-mode data format

PCT uses its own data format to store list-mode proton CT data as MetaImage files (.mhd or .mha extension). The data corresponds to so-called proton pairs information (position, direction, energy, …), i.e. the information recorded by the entrance and exit detectors which are paired, e.g. by a coincidence electronics or by an algorithm.

Some PCT executables produce such data, e.g. pctpairprotons from ROOT data produced by a GATE simulation, whereas other ones take such data as input, e.g. pctbinning. PCT uses an ITK image internally (itk::Image) to read from / write to these MetaImage files.

Proton pairs are stored in 2D images of 3D float vectors, in which the first dimension is a series of 5 or 6 vectors of 3 floats each, one per proton pair, and the second dimension corresponds to the number of proton pairs. Each vector stores the following data:

  1. \((u_{\text{in}},v_{\text{in}},w_{\text{in}})\) position of the proton at the entrance detector;

  2. \((u_{\text{out}},v_{\text{out}},w_{\text{out}})\) position of the proton at the exit detector;

  3. \((\dot u_{\text{in}}, \dot v_{\text{in}}, \dot w_{\text{in}})\) direction of the proton at the entrance detector (as unit vector);

  4. \((\dot u_{\text{out}}, \dot v_{\text{out}}, \dot w_{\text{out}})\) direction of the proton at the exit detector (as unit vector);

  5. \((e_{\text{in}},e_{\text{out}},t)\) where

    • \(e_{\text{in}}\) and \(e_{\text{out}}\) are the proton energy at the entrance and exit detectors, respectively.

      • Important note 1: if \(e_{\text{in}}=0\), then \(e_{\text{out}}\) will directly be interpreted as the water equivalent path length (WEPL) for the proton pair.

      • Important note 2: \(e_{\text{in}}\) and \(e_{\text{out}}\) can alternatively represent the time of detection of the protons, if pctpairprotons was executed using the --store-time flag.

    • \(t\) is not used in PCT but can be used to store some useful scalar such as the GATE TrackID in pctpairprotons.

  6. Optionally, mainly for the work in http://doi.org/10.1088/0031-9155/61/9/3258 \((\text{creatorProcess}, \text{nuclearProcess}, \text{order})\) are used in simulations to indicate

    • the process which created the exit particle,

    • whether the particle did encounter a nuclear interaction,

    • the number of particle interactions.

Note that PCT assumes that the proton beam goes along the \(w\) axis in the positive direction (\(w_{\text{in}} < w_{\text{out}}\)).