TgtLocFile = fullfile( dataDir, 'tgt_slice_no.txt ' ) ĮxcludeSliceFile = fullfile( dataDir, 'force_exclude_slice.txt ' ) ĮxcludeSlice = fscanf( fid, ' %f ' ) + 1 % NOTE: slice locations in input file are zero-indexed fclose( fid ) Įnd % slice-slice cardiac synchronisation M = matfile( fullfile( cardsyncDir, 'results_cardsync_intraslice.mat ' ) ) Note: if using the demo dataset, Part 0 can be skipped.ĬardsyncDir = fullfile( reconDir, 'cardsync ' ) ĬineDir = fullfile( reconDir, 'slice_cine_vol ' ) vtk files can be manually loaded into Paraview. A final step using Python is performed to automate visualisation of the 4D flow volumes in Paraview, however, this is optional as the. The reconstruction process is performed using a combination of Matlab and bash scripts which call various C++ functions in the SVRTK toolbox. background drift correction of 4D velocity volumes.4D velocity cine volume reconstruction and.gradient first moment reorientation to account for motion with respect to the velocity-encoding gradients.background phase correction of phase images.4D magnitude cine volume reconstruction, including outlier rejection.further motion-correction using dynamic image frames interleaved with 4D reconstruction and.cardiac synchronisation, including heart rate estimation and slice-slice cardiac cycle alignment and.an initial motion correction stage to achieve rough spatial alignment of the fetal heart using temporal mean (i.e., static) images for stack-stack registration followed by slice-volume registration interleaved with static volume (3D) reconstruction.multiple stacks of real-time non-coplanar 2D bSSFP slices are acquired using a 1.5T MRI scanner and reconstructed offline using ReconFrame.PART 0 (2D MRI Acquisition and k-t SENSE Reconstruction): This framework produces 4D magnitude and velocity cine volumes. Similarly, we provide the gradient first moment text files, which we would normally automatically generate using ReconFrame. Note: the nifti files provided in the demo dataset have been reconstructed using the ktrecon submodule, which requires ReconFrame. The expected run time for the demo, from slices to 4D volumes, is 6+ hours depending on computer power and familiarity with the concepts and scripts. The script comprises various Matlab functions and tells the user when to run the bash scripts. A Matlab script is included alongside the demo dataset, which follows the 4D reconstruction framework outlined below. The demo dataset consists of multiple stacks of 2D slices acquired in a normal fetus. ReconFrame - software platform providing the tools and the functionality to develop and execute a complete image reconstruction of Philips MR data ( /gt/index.php/products/reconframe) Demo DatasetĪ demo dataset can be downloaded from Figshare. Typically everything can be installed in less than one hour. Installation time varies depending on how many libraries and programs you already have installed. Note, version 5.4.1 is known to be stable. Install Paraview for visualisation of 4D flow volumes:. Note, 2016.11 version is known to be stable.įor Python code, install Jupyter or P圜harm. Install MITK Workbench for viewing data and drawing masks: /wiki/The_Medical_Imaging_Interaction_Toolkit_(MITK). Synthflow_phantom - simulated flow phantom and 2D velocity-encoded slice acquisition submodule linked to /tomaroberts/synthflow_phantom Installationīuild instructions for SVRTK can be found in the InstallationInstructions.txt file at /SVRTK/SVRTK. Paraview - visualisation of 4D flow volumes Ktrecon - k-t sense reconstruction submodule linked to /mriphysics/ktrecon SVRTK - 4D reconstruction submodule linked to /SVRTK/SVRTK arXiv: 1812.02249 ( preprint) DirectoriesĤdflow - preprocessing and postprocessing scripts for flow reconstructionĤdrecon - preprocessing and 4D reconstruction scripts Joshua FP van Amerom, David FA Lloyd, Maria Deprez, Anthony N Price, Shaihan J Malik, Kuberan Pushparajah, Milou PM van Poppel, Mary A Rutherford, Reza Razavi, Joseph V Hajnal. Hajnal.įetal whole-heart 4D imaging using motion-corrected multi-planar real-time MRI Jackson, Shaihan J Malik, Milou PM van Poppel, Kuberan Pushparajah, Mary A Rutherford, Reza Rezavi, Maria Deprez, Joseph V. Price, Jacques-Donald Tournier, Laurence H. Roberts, Joshua FP van Amerom, Alena Uus, David FA Lloyd, Anthony N. Fetal whole-heart 4D magnitude and flow cine reconstruction using multiple real-time non-coplanar balanced SSFP stacksįetal whole-heart 4D flow cine MRI using multiple non-coplanar balanced SSFP stacks
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