Title: Simulated simultaneous 18F-NaF PET/MR with physiological motion and ground truth information
Authors: Mayer, Johannes, Physikalisch-Technische Bundesanstalt (PTB), Fachbereich 8.1, Biomedizinische Magnetresonanz, ORCID: 0000-0002-2500-445X
Kolbitsch, Christoph, Physikalisch-Technische Bundesanstalt (PTB), Fachbereich 8.1, Biomedizinische Magnetresonanz, ORCID: 0000-0002-4355-8368
Contributors: HostingInstitution: Physikalisch-Technische Bundesanstalt (PTB), ISNI: 0000 0001 2186 1887
Language:en
DOI:10.7795/710.20201113
Resource Type: Dataset / Simulation Data
Publisher: Physikalisch-Technische Bundesanstalt (PTB)
Rights: https://creativecommons.org/licenses/by/4.0/
CC BY 4.0 International
Relationships: IsReferencedBy: DOI https://doi.org/10.1016/j.cpc.2019.107087
IsReferencedBy: DOI https://doi.org/10.1088/1361-6560/ab7eee
Dates: Available: 2020-11-19
Created: 2020-11-02
Classifications: INSPEC A4230V Image processing and restoration ; INSPEC A8760K Nuclear medicine, emission tomography ; INSPEC A8760I Medical magnetic resonance imaging and spectroscopy
File: Download File (application/zip) 777.44 MB (815200333 Bytes)
MD5 Checksum: afeb2ae8fb93de859c6ad8a74d798470
SHA256 Checksum: 4c65d059fafa957a381161a867bd2ee11f06f5e7a8d61c1f1548e1342b1f5420
Keywords: PET-MR ; NaF-PET ; Coronary artery disease ; cardiac motion ; respiratory motion ; motion-corrected image reconstruction
Abstract: This dataset is the basis for the publication "Evaluation of synergistic image registration for motion-corrected coronary NaF-PET-MR"
Dataset containing simulated cardiac and respiratory motion of simultaneous PET/MR data with 18F-NaF uptake in the right coronary artery.
Supplied are PET and MR images, as well as underlying ground truth motion and regions of interests (ROI) in which the uptake and background signal are located.
The dataset is based on the XCAT phantom and a custom simulation integrated into the Syngergistic Image Reconstruction Framework (SIRF, doi:10.1016/j.cpc.2019.107087 and 10.1088/1361-6560/ab7eee)
Each sub-folder contains data for one motion type, either respiration or heartbeat, with the same respective file names.

Description of the individual files:

All files are in the nifti file format.
The geometry information in the nifti header carries no meaning for this dataset wrt patient orientation and voxel sizes etc.
It only keeps track of the data sizes. The geometry of all the supplied files match already and require no transformation.

The voxel size is (1.5mm)*(1.5mm)*(1.5mm) spatially isotropic.

The data can be read into Python using for example the package nibabel.
The data can be read also by image viewers such as ImageJ.

File list:

- naf_mri_image_series.nii

reconcstructed image series simulated cardiac 3T MRI of FLASH contrast, with contrast agent and fat suppression. The image intensity is in arbitrary units.
datasize: 192 192 192 4 = Nx, Ny, Nz, Nt (Nt = # of reconstructed motion states)

- activity(12/25/50/100)_naf_pet_image_series.nii
reconcstructed image series simulated cardiac PET with NaF uptake in right coronary artery. Reconstruction without attenuation correction. The image intensity is in arbitrary units.
datasize: 192 192 192 4 = Nx, Ny, Nz, Nt

- naf_gt_imf.nii
ground truth motion information underlying the simulation.
The imf for the different motion states t=0,...Nt-1 are displacement vector fields such that i(r,t) = i(r + naf_gt_imf(r,t),0) for = naf_mri_image_series or activity(12/25/50/100)_naf_pet_image_series
datasize: 192 192 192 3 4 = Nx, Ny, Nz, Nv, Nt, (Nv = spatial dimensions)
The unit of the motion field is in voxels, not millimeters.

- signal_roi.nii
ROI in which the NaF uptake signal was evaluated
This ROI is in the motion state t=0
datasize: 192 192 192 = Nx, Ny, Nz

- background_roi.nii
ROI in which the background signal was evaluated
This ROI is in the motion state t=0
datasize: 192 192 192 = Nx, Ny, Nz
Other: EMPIR projects are co-funded by the European Union’s (EU) Horizon 2020 research and innovation programme and the EMPIR participating states.
Funding: Deutsche Physikalischalische Gesellschaft (DFG), ISNI: 0000 0001 2096 9829, Grant Title: BIOphysical Quantitative Imaging Towards Clinical Diagnosis, Grant Number: GRK 2260 BIOQIC
Deutsche Physikalischalische Gesellschaft (DFG), ISNI: 0000 0001 2096 9829, Grant Title: In vivo Visualisierung der pathologisch veränderten Extrazellulärmatrix, Grant Number: SFB 1340 Matrix in Vision