STIR2PETSIRD converter

The purpose of this repo is to provide a starting point for converting list mode PET data read by STIR to PETSIRD.

Background

The Emission Tomography Standardization Initiative (ETSI) is working towards establishing a standard for PET Raw Data, called PETSIRD ("PET ETSI Raw Data"). More information is on https://github.com/ETSInitiative/PETSIRD.

Status

This is still work in progress, but does seem to work, including normalisation (no singles nor dead-time info is passed on).

Installation

Either use the devcontainer, or self-build:

git clone --recurse-submodules https://github.com/ETSIhackers/STIR2PETSIRD.git
cd STIR2PETSIRD
conda env create
conda activate petsird
just build

This will install the executable in $CONDA_PREFIX/bin. If you want it installed somewhere else, you can specify the value of CMAKE_INSTALL_PREFIX as an argument:

just build ~/my_install_directory

Example usage

For the mMR acquisition of the NEMA phantom on Zenodo:

1. fix the EOL conventions in the Siemens .n.hdr

   sed -i.bak 's/\r\([^\n]\)/\r\n\1/g' < 20170809_NEMA_UCL.n.hdr > 20170809_NEMA_UCL.n.hdr.fixedEOL
   
   

2. create a file norm.par

   Bin Normalisation parameters:=
   type:= From ECAT8
    Bin Normalisation From ecat8 :=
    normalisation filename:= 20170809_NEMA_UCL.n.hdr.fixedEOL
    End Bin Normalisation From ecat8:=
   END:=
   

3. run the convertor

   STIR_PETSIRD_convertor  mMR_NEMA_norm.petsird 20170809_NEMA_60min_UCL.l.hdr norm.par