Gentle Warning --- Old Repo

Hello! I am going to phase out this repo and consolidate everything into the fetal_cmr_4d repo: https://github.com/tomaroberts/fetal_cmr_4d.

The recommended and most stable fetal CMR 4D reconstruction repo can be found here: https://github.com/mriphysics/fetal_cmr_4d

fetal_cmr_4dflow

fetal whole heart 4D flow cine MRI using multiple non-coplanar balanced SSFP stacks

Publications

Fetal whole-heart 4D flow cine MRI using multiple non-coplanar balanced SSFP stacks
Thomas A. Roberts, Joshua FP van Amerom, Alena Uus, David FA Lloyd, Anthony N. Price, Jacques-Donald Tournier, Laurence H. Jackson, Shaihan J Malik, Milou PM van Poppel, Kuberan Pushparajah, Mary A Rutherford, Reza Rezavi, Maria Deprez, Joseph V. Hajnal.

bioRxiv. 2019. doi: https://doi.org/10.1101/635797 (pre-print)

Directories

4dflow_recon - pre- and post-processing scripts for 4D cine flow reconstruction

lib - sub-functions and scripts

paraview - visualisation of 4D cine flow volumes in Paraview: [https://www.paraview.org/]

matlab-common - submodule containing useful MATLAB scripts (nb: when cloning this repo, use command line option --recurse-submodules )

Dependencies

SVRTK - slice-to-volume registration reconstruction software. Similar to IRTK, but now compatible with MIRTK. Download SVRTK here: https://github.com/SVRTK/SVRTK

4d_recon - 4D magnitude cine reconstruction code. Parameters from magnitude reconstruction are passed to the 4D flow reconstruction. Download here: https://github.com/jfpva/fetal_cmr_4d

Installation

For MATLAB scripts, add everything to MATLAB path.

For Paraview visualisation, run the .py file using pvpython.exe within your Paraview install directory.

4D Flow Cine Framework

The 4D flow cine reconstruction framework is an extension of the 4D magnitude cine framework developed by van Amerom et al.: https://github.com/jfpva/fetal_cmr_4d

See Also

Code for synthetic flow phantom used in this paper: https://github.com/tomaroberts/synthflow_phantom