These scripts reproduce the experiments described in the article:
Rosenzweig S, Scholand N, Holme HCM, Uecker M.
Cardiac and Respiratory Self-Gating in Radial MRI using an Adapted Singular Spectrum Analysis (SSA-FARY).
IEEE Trans Med Imag 2020, Early Access, DOI: 10.1109/TMI.2020.2985994 [1,2]
The algorithms have been integrated into the Berkeley Advanced Reconstruction Toolbox (BART) [3] (commit 737082541c).
The raw files are hosted on ZENODO and must be downloaded first
- Manual download: https://zenodo.org/record/3822451
- Download via script: Run the download script in the ./data folder.
- All files:
bash load_all.sh - Individual files:
bash load.sh 3822451 <FILENAME> .( without file extension. Then extract the *.tgz)
- All files:
- Note: The data must be stored in the ./data folder
The other folders contain:
- run.sh scripts, which perfoms the image reconstruction
- plot.sh scripts, which create the Figures
- makemovie.sh scripts, which create the movie files
- some *.py scripts for plotting tasks
- and a results folder, with images and movies that serve as reference
To run the scripts GNU Bash [4] is required.
The data can be viewed e.g. with 'view'[5] or be loaded into Matlab or Python using the wrappers provided in BART subdirectories './matlab' and './python'
To reproduce the plots and figures python3 [6], the 'cfl2png' command from _view [5], and 'convert' from imagemagick [7] and the Linux Biolinum font [8] are required. The font can be downloaded by running the get_font.sh script in the utils folder. To create the movies ffmpeg [9] is used.
Please note that BART with GPU support is required. Running all scripts will take more than 24 hours, even on a multi-core compute system!
If you need further help to run the scripts, I am happy to help you: [email protected]
Mai 14, 2020 - Sebastian Rosenzweig
[1] https://ieeexplore.ieee.org/document/9057630 (DOI: 10.1109/TMI.2020.2985994, early access) [2] https://arxiv.org/abs/1812.09057v6 [3] https://mrirecon.github.io/bart [4] https://www.gnu.org/software/bash/ [5] https://github.com/mrirecon/view [6] https://www.python.org [7] https://imagemagick.org [8] https://www.fontsquirrel.com/fonts/linux-biolinum [9] https://ffmpeg.org