• Files included
• Inveon data in OMEGA
  • Remarks on reconstruction

This page describes the contents of the open Siemens Inveon PET data and how to use it. The data can be obtained from: https://doi.org/10.5281/zenodo.3528056. Alternatively, you can use the NEMA phantom data from https://doi.org/10.5281/zenodo.4646897.

FDG_Naive_R01_PET_Em_F18_60min_v1.lst is the raw list-mode data. Each event is stored in binary format with the tag related information. For decrypting the list-mode data itself, you should contact Siemens. A header file is also included that has some general information on the measurement and the device.

FDG_Naive_R01_PET_Em_F18_60min_v1.scn contains the sinogram created by the PET scanner/acquisition computer itself. Randoms correction has already been included in the form of subtraction. This sinogram is dynamic and contains 28 frames. A header file is included that contains more detailed information on the file.

FDG_Naive_R01_PET_Em_F18_60min_v1_sct.scn this is the scanner created dynamic SCATTER sinogram. Format is exactly the same as the regular sinogram. This should be used for potential scatter correction.

FDG_Naive_R01_PTX_At_10min_v1.atn this contains the attenuation data. This cannot be used as-is. In OMEGA this measurement data is reconstructed and then used in the attenuation correction, by using the reconstructed images as the attenuation images.

Norm_PNM_Normalization_with_Cylinder_v1.nrm is the normalization data. The inverse of this should be multiplied with the sinogram for normalization correction (when normalization is not included in the reconstruction). In OMEGA, this can be used as the user normalization.

When using the Inveon data in OMEGA, one should use Inveon_PET_main.m file. All the geometry and sinogram values have been adjusted just as the defaults are. This file includes support for GATE data, so when using the list-mode or sinogram data all the GATE specific sections can be ignored. By default the main file has enabled list-mode data, randoms correction, attenuation correction, normalization correction using the provided normalization (.nrm) file and uses sinogram data for reconstruction with 128x128x159 resolution. Scatter correction is NOT enabled by default.

Inveon data format is chosen in the second block/section below SCANNER PROPERTIES (INVEON DATA). Here you can specify whether to use GATE data (options.use_machine = 0), the list-mode (.lst) data (options.use_machine = 1, default) or sinogram (.scn) data (options.use_machine = 2). For the list-mode case, the user will be prompted for the location of the list-mode data file when load_data is run. For the sinogram case, the prompt will be during sinogram formation (form_sinograms). Using GATE data works just as with any other GATE data.

When using any corrections, same rules and features apply as with any data.

If options.randoms_correction is set to true, then the delayed coincidences will be automatically loaded when the prompts are loaded as well.

When using scatter correction, you can use the provided scn-files when prompted for the scatter data. Scatter data will be prompted FIRST, if you have it enabled.

If you are using the provided SINOGRAM (.scn) file instead of the list-mode file, in static cases the dynamic sinograms are summed together. However, if dynamic reconstruction is performed, then the number of time steps needs to be same as in the sinogram (28) or less. If you create your own sinogram or raw data from the list-mode file, you can specify any number of time steps.

Normalization is included if options.normalization_correction = true. In order to use the provided .nrm-file then you should set options.use_user_normalization = true. The user will then be prompted for the normalization file (.nrm) either during sinogram creation (if options.corrections_during_reconstruction = false) or right before image reconstruction is initiated. If options.use_user_normalization = false, then OMEGA will attempt to find user-created normalization (.mat) file, i.e. normalization file created by OMEGA.

For attenuation correction, first options.attenuation_correction must be set to true and secondly the section containing the function (or the function itself) attenuation_correction_factors needs to be run. The user will then be prompted to select the provided .atn-file. The function will then save a mat-file containing the attenuation images reconstructed from the attenuation sinogram. The output is the filename of this mat-file which is needed during the image reconstruction phase. By default, no additional actions are needed from the user. For future use, it is recommended to modify options.attenuation_datafile path after options.attenuation_correction to the path of the saved attenuation datafile. Filename itself is enough if the file is in MATLAB search path, i.e. current directory which is the default.

If you are using your own Inveon data and have access to Inveon CT, you can also use the created UMAP-images as the attenuation correction. This can be enabled by setting options.use_CT = true and running the aforementioned attenuation_correction_factors.