rtspiral_pypulseq
2D and 3D Real-time Spiral sequences with PyPulseq
Science Score: 75.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 8 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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✓Institutional organization owner
Organization usc-mrel has institutional domain (mrel.usc.edu) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary
Repository
2D and 3D Real-time Spiral sequences with PyPulseq
Basic Info
Statistics
- Stars: 0
- Watchers: 5
- Forks: 1
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
2D/3D Spiral Sequences with PyPulseq
Installation
Create a Python environment with your favorite tool (venv, conda, pyenv). For venv:
python -m venv venv
Activate your environment. For example, for venv:
source venv/bin/activate
Install the dependencies:
pip install -r requirements.txt
Last command should compile and put the libraries to the necessary places.
Note: On some systems (Ubuntu), following package may need to be installed for Qt to work:
sudo apt install libxcb-cursor0
Dependencies
See requirements.txt.
gropt is optional. If it is not possible to compile it for your system, please use the other rewinder design methods. Note that there are small changes to the Python code of the library as bug fixes.
Usage
Configuration
Copy example_config.toml and rename it as config.toml.
systems/ contains example scanner specs to copy paste into config.toml [system] part.
Run write_rtspiral.py to generate the trajectory and metadata.
Outputs
When write_seq = true in config.toml, a .seq file will be generated in the out_seq/ directory, and the corresponding metadata, which will be named as the sequence_hash.mat as a .mat file will be put into out_trajectory/ directory.
References and Acknowledgements
Variable-Density Spiral Design Functions by Brian Hargreaves - http://mrsrl.stanford.edu/~brian/vdspiral/
- Hoge RD, Kwan RKS, Pike GB. Density compensation functions for spiral MRI. Magnetic Resonance in Medicine. 1997;38(1):117-128. doi:10.1002/mrm.1910380117
- Loecher M, Middione MJ, Ennis DB. A gradient optimization toolbox for general purpose time-optimal MRI gradient waveform design. Magnetic Resonance in Medicine. 2020;84(6):3234-3245. doi:10.1002/mrm.28384
- Lee JH, Hargreaves BA, Hu BS, Nishimura DG. Fast 3D imaging using variable-density spiral trajectories with applications to limb perfusion. Magnetic Resonance in Medicine. 2003;50(6):1276-1285. doi:10.1002/mrm.10644
- Ibrahim ESH, Stuber M, Schär M, Osman NF. Improved myocardial tagging contrast in cine balanced SSFP images. Journal of Magnetic Resonance Imaging. 2006;24(5):1159-1167. doi:10.1002/jmri.20730
- Chen W, Lee NG, Byrd D, Narayanan S, Nayak KS. Improved real-time tagged MRI using REALTAG. Magnetic Resonance in Medicine. 2020;84(2):838-846. doi:10.1002/mrm.28144
- Pipe JG, Zwart NR. Spiral trajectory design: A flexible numerical algorithm and base analytical equations. Magnetic Resonance in Medicine. 2014;71(1):278-285. doi:10.1002/mrm.24675
Owner
- Name: Magnetic Resonance Engineering Laboratory
- Login: usc-mrel
- Kind: organization
- Location: Los Angeles, California
- Website: http://mrel.usc.edu
- Twitter: nayak_lab
- Repositories: 31
- Profile: https://github.com/usc-mrel
Magnetic Resonance Engineering Laboratory, University of Southern California
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Tasdelen" given-names: "Bilal" orcid: "https://orcid.org/0000-0001-6462-3651" - family-names: "Kumar" given-names: "Prakash" orcid: "https://orcid.org/0000-0002-0685-5160" title: "2D/3D Spiral Sequences with PyPulseq" version: 0.9 doi: 10.5281/zenodo.15284023 date-released: 2023-11-26 url: "https://github.com/usc-mrel/rtspiral_pypulseq"
GitHub Events
Total
- Create event: 7
- Issues event: 1
- Release event: 2
- Watch event: 1
- Delete event: 3
- Issue comment event: 7
- Push event: 40
- Pull request review comment event: 6
- Pull request review event: 4
- Pull request event: 8
- Fork event: 1
Last Year
- Create event: 7
- Issues event: 1
- Release event: 2
- Watch event: 1
- Delete event: 3
- Issue comment event: 7
- Push event: 40
- Pull request review comment event: 6
- Pull request review event: 4
- Pull request event: 8
- Fork event: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 1
- Total pull requests: 5
- Average time to close issues: N/A
- Average time to close pull requests: about 1 hour
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.2
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 5
- Average time to close issues: N/A
- Average time to close pull requests: about 1 hour
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.2
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Tooine (1)
Pull Request Authors
- btasdelen (5)
- pkash16 (2)
- dependabot[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- Pillow ==10.1.0
- PySide2 ==5.13.2
- cffi ==1.16.0
- contourpy ==1.2.0
- cycler ==0.12.1
- fonttools ==4.45.0
- kiwisolver ==1.4.5
- matplotlib ==3.8.2
- numpy ==1.26.2
- packaging ==23.2
- pycparser ==2.21
- pyparsing ==3.1.1
- python-dateutil ==2.8.2
- seaborn *
- sigpy ==0.1.26
- six ==1.16.0
- tomli >=1.1.0
- cffi *
- matplotlib *
- numpy *
- MRzeroCore *
- PySide6 *
- cupy-cuda12x *
- ipympl *
- ipython *
- jupyterlab *
- matplotlib *