Jaszczak pipeline

This pipeline helps you to choose the best reconstruction for a PET camera by quantifying activity in jaszczak's spheres.

Before using this pipeline:
  1. Define your jaszczak if it is a new one.
  2. Import your CT and PET Dicom images
  3. Convert your dicom images into nii format.
All this steps can be openned separatly, using right click.

Finally, you can use this pipeline by selecting just your CT image (others parameters are automatically deducted).

Description

The Jaszczak SPECT Phantom provides consistent performance information for any SPECT or PET system.
  • D : radioactivity is injected in spheres called "hot spheres", the others are "cold" ( you can see these ones in black). Then the activity in spheres' image is quantified and compare with the theoretical one, for each reconstruction. A graph allows you to compare reconstructions
  • E : Rods are used to check visually the image resolution. To do so, all slices with rods are summed.

    • To quantify spheres:
    To quantify the activity in Jaszczak's spheres, you need to fill the fields about the activity injected in Jaszczak and its spheres.quantify spheres.

    Pipeline steps' details :

  • The acquisition can be dynamic, so the mean is computed (step 1)
  • All PET images and the CT one are segmented to check a possible gap between them. (step 2 Segment sph PET , 3 Segment sph CT, 4 Check fusion PET CT) Note : If so, the camera should be fixed.
  • According to this gap, the spheres' mask is computed (step 5 Build Sph Mask) and used to quantify spheres (step 7 Quantify spheres)
  • All slices with rods are summed and then displayed, to check visually the resolution (step 6 Sum rods)
  • All reconstructions are quantified (step 7 Quantify spheres), using ROI previously computed and AimsRoiFeatures
  • All reconstructions can be compared thanks to the graphic computed in step 8 Compare quantification

    • Pipeline steps' documentation :

    Spheres Segmentations :

    Segment sph PET

    Segment sph CT

    Check fusion PET CT

    Build Sph Mask

    Display CT, PET, ROI and Mask fusions

    Reconstruction Comparison :

    Sum rods

    Quantify spheres

    Compare quantification

    Display reconstructions comparison

    Parameters

    database: Choice ( input )
    display_separatly_each_process: Choice ( input )
    Pets_mean: ListOf( Phantom PET Mean ) ( input )
    CT: Phantom CT ( input )
    phantom: String ( input )
    center: String ( input )
    jzkSpec: Phantom Spec ( input )
    theoric_values: Phantom Theoric Values ( optional, output )
    bkg_preparedActivity: Float ( input )
    prepared activity in background unit is Mega bequerel
    bkg_H_M_pre: String ( input )
    bkg_residualActivity: Float ( input )
    residual activity in background unit is Mega bequerel
    bkg_H_M_res: String ( input )
    sph_preparedActivity: Float ( input )
    prepared activity in spheres unit is Mega bequerel
    sph_H_M_pre: String ( input )
    sph_residualActivity: Float ( input )
    residual activity in spheres unit is Mega bequerel
    sph_H_M_res: String ( input )
    H_M_acq: String ( input )
    periode_isotope: Float ( input )
    run_parallel: Boolean ( input )
    verbose: Boolean ( input )
    reconstructionNames: ListOf( String ) ( input )
    Pets_segmented: ListOf( Phantom PET Mean Segmented ) ( output )
    ct_segmented: Phantom CT Segmented ( output )
    sph_rois: Phantom ROI Sph ( optional, output )
    sph_roi_in_Noise: Phantom ROI Sph inNoise ( output )
    PET_mean_toDisplay: Phantom PET Mean ( output )
    Pet_segmented_toDisplay: Phantom PET Mean Segmented ( output )
    CT2PetMeans: ListOf( CT to PET transformation file ) ( output )
    PETs_ghosts: ListOf( Phantom ROI Sph Ghosts ) ( output )
    allRods: ListOf( Phantom Rods ) ( output )
    allRods_sum: ListOf( Phantom Rods Sum ) ( output )
    stats_inSpheres: ListOf( Phantom Activity Stats ) ( output )
    stats_inNoise: ListOf( Phantom Noise Stats ) ( output )
    stats_inGhosts: ListOf( Phantom ROI Sph Ghosts Stat ) ( output )
    ratios_inSpheres: ListOf( Phantom Result ) ( output )
    ratios_inGhosts: ListOf( Phantom Sph Ghosts Result ) ( output )
    graph: Phantom Graph HotSph ( output )
    graph_coldSph: Phantom Graph ColdSph ( output )
    Spheres_ID_PVC: ListOf( Integer ) ( input )
    Spheres_ID_FWHM: ListOf( Integer ) ( optional, input )
    selected_FWHM_prieto: String ( optional, input )
    selected_FWHM_normal: String ( optional, input )
    selected_FWHM_special: String ( optional, input )
    ROI_folders_list: ListOf( Phantom ROI PVC ) ( optional, output )
    FWHM_informations_files_list: ListOf( FWHM Informations Jaszczak ) ( optional, output )
    Chi_curves_folders_list: ListOf( Chi Square folder ) ( optional, output )
    Corrected_uptakes_list: ListOf( Phantom PVC Corrected Uptakes Stats ) ( optional, output )
    RC_calculation_method: Choice ( optional, input )
    PVC_method: Choice ( optional, input )
    Fill_centers: Choice ( optional, input )
    CT_sph1_center: Point3D ( optional, input )
    CT_sph2_center: Point3D ( optional, input )
    CT_sph3_center: Point3D ( optional, input )
    CT_sph4_center: Point3D ( optional, input )
    CT_sph5_center: Point3D ( optional, input )
    CT_sph6_center: Point3D ( optional, input )
    PVC_dictionary: PVC Jaszczak dictionary ( optional, output )

    Technical information

    Toolbox : Nuclear Imaging

    User level : 0

    Identifier : JZKPipeline

    File name : brainvisa/toolboxes/nuclearimaging/processes/JZKPipeline.py

    Supported file formats :

    Pets_mean :
    NIFTI-1 image, NIFTI-1 image
    CT :
    NIFTI-1 image, NIFTI-1 image
    jzkSpec :
    CSV file, CSV file
    theoric_values :
    CSV file, CSV file
    Pets_segmented :
    NIFTI-1 image, NIFTI-1 image
    ct_segmented :
    NIFTI-1 image, NIFTI-1 image
    sph_rois :
    NIFTI-1 image, NIFTI-1 image
    sph_roi_in_Noise :
    NIFTI-1 image, NIFTI-1 image
    PET_mean_toDisplay :
    NIFTI-1 image, NIFTI-1 image
    Pet_segmented_toDisplay :
    NIFTI-1 image, NIFTI-1 image
    CT2PetMeans :
    Transformation matrix, Transformation matrix
    PETs_ghosts :
    NIFTI-1 image, NIFTI-1 image
    allRods :
    NIFTI-1 image, NIFTI-1 image
    allRods_sum :
    NIFTI-1 image, NIFTI-1 image
    stats_inSpheres :
    CSV file, CSV file
    stats_inNoise :
    CSV file, CSV file
    stats_inGhosts :
    CSV file, CSV file
    ratios_inSpheres :
    CSV file, CSV file
    ratios_inGhosts :
    CSV file, CSV file
    graph :
    CSV file, CSV file
    graph_coldSph :
    CSV file, CSV file
    ROI_folders_list :
    Directory, Directory
    FWHM_informations_files_list :
    Text file, Text file
    Chi_curves_folders_list :
    Directory, Directory
    Corrected_uptakes_list :
    CSV file, CSV file
    PVC_dictionary :
    Text file, Text file