# hyperpolarized-mri-toolbox
<img src="hyperpolarized-mri-toolbox_logo.png" width="20%" height="20%">
The goal of this toolbox is to provide research-level and prototyping software tools for hyperpolarized MRI experiments. It is currently based on MATLAB code, and includes code for designing radiofrequency (RF) pulses, readout gradients, data reconstruction, and data analysis.
It is hosted on this open-source, collaborative platform in order to encourage anyone and everyone in the hyperpolarized MRI research community to contribute tools that will help our field rapidly progress.
## Citations
```
Hyperpolarized-MRI-Toolbox.
Available online at: https://github.com/LarsonLab/hyperpolarized-mri-toolbox
https://dx.doi.org/10.5281/zenodo.1198915
```
```
Crane, JC, Gordon, JW, Chen, H-Y, Autry AW, Li Y, Olson MP, Kurhanewicz J, Vigneron DB, Larson PEZ, Xu D.
Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco.
NMR in Biomedicine. 2021; 34:e4280. https://doi.org/10.1002/nbm.4280
```
## Getting Started
1. Download latest release (at right) and extract or clone git repository (via 'Code' at the top)
1. Open Matlab or Octave
1. Navigate to the `hyperpolarized-mri-toolbox/` directory
1. Run `startup`. This will setup path and confirm you have required toolboxes
### Examples and Exercises
There are starter code and examples in
* `hyperpolarized-mri-toolbox/demo_notebooks/`
* `hyperpolarized-mri-toolbox/RF_pulses/spectral_spatial/examples/`
There are also several exercises to learn working with the data, analysis functions, and spectral-spatial RF pulse design in
* `hyperpolarized-mri-toolbox/exercises/`
### MyBinder online demos
You can also run the demo jupyter notebooks online without installing or downloading the code through MyBinder:
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/LarsonLab/hyperpolarized-mri-toolbox/master?filepath=demo_notebooks)
Note that it may take several minutes to build if this has not been used in a while.
### Requirements
#### MATLAB
Toolboxes: Optimization, Image Processing
#### Octave
Toolboxes: ptim, image, io, statistics, signal
Missing functionality in Octave in spectral-spatial RF pulse design
## Hyperpolarized Metabolic MRI Seminar
For general education on hyperpolarzed carbon-13 metabolic MRI, lectures and slides from the UCSF Hyperpolarized MR Seminar (summer 2019) are available
* (HP MRI Course 2021) https://hyperpolarizedmri.ucsf.edu/hp-mri-course-2021
* (HP MRI Course 2019) https://www.youtube.com/playlist?list=PLjBt5Iq93BT-vODpVTT5R-uOB-MYaSZOn
* https://www.slideshare.net/PederLarson1
## Related Tools
### Visualization and Implemented Pipelines: SIVIC
This toolbox is jointly developed with the Spectrscopic Imaging VIsualization and Computing (SIVIC) framework (https://sourceforge.net/projects/sivic/), which is also hosted on [github](https://github.com/SIVICLab/sivic).
While this toolbox focuses on prototyping new methods, leveraging the flexibility of MATLAB to rapidly perform this work, while SIVIC is focused on deployment of methods once they have been validated and also has focused on providing data visualization tools (e.g. mix of spectroscopy, imaging, 1H reference images, and parameter maps). SIVIC is more suited for use in routine hyperpolarized MR studies.
### Pulse Sequences
The UCSF Hyperpolarized MRI Technology Resource Center (https://hyperpolarizedmri.ucsf.edu/, NIH Grant P41-EB013598) has specialized hyperpolarized 13C pulse sequences available, including Metabolite-specific EPI (GE), Metabolite-specific Spirals with real-time calibration (RTHawk) as well as several for Bruker and Varian small animal systems. Please reach out through the center for more information.
### Spectral-Spatial-RF-Pulse-Design toolbox
This includes, as a subtree, the
[Spectral-Spatial-RF-Pulse-Design toolbox](https://github.com/LarsonLab/Spectral-Spatial-RF-Pulse-Design) for hyperpolarized MRI RF pulse design. For reference, here's how to update the subtree with git:
(run from root directory of hyperpolarized-mri-toolbox)
git subtree add --prefix RF_pulses/spectral_spatial https://github.com/LarsonLab/Spectral-Spatial-RF-Pulse-Design.git master --squash
git subtree pull --prefix RF_pulses/spectral_spatial https://github.com/LarsonLab/Spectral-Spatial-RF-Pulse-Design.git master --squash
git subtree push --prefix RF_pulses/spectral_spatial https://github.com/LarsonLab/Spectral-Spatial-RF-Pulse-Design.git master --squash
## Support
This toolbox was created as a part of the UCSF Hyperpolarized MRI Technology Resource Center (https://hyperpolarizedmri.ucsf.edu/) which is funded by the National Institutes of Health (NIH Grant P41-EB013598).
Please let us know if you would like to contribute or have suggestions for content, contact Peder Larson, University of California - San Francisco
没有合适的资源?快使用搜索试试~ 我知道了~
超极化磁共振成像matlab工具箱.zip
共1082个文件
dcm:744个
m:196个
mat:79个
1.该资源内容由用户上传,如若侵权请联系客服进行举报
2.虚拟产品一经售出概不退款(资源遇到问题,请及时私信上传者)
2.虚拟产品一经售出概不退款(资源遇到问题,请及时私信上传者)
版权申诉
0 下载量 95 浏览量
2024-02-21
23:21:54
上传
评论
收藏 124.15MB ZIP 举报
温馨提示
1.版本:matlab2014/2019a/2021a 2.附赠案例数据可直接运行matlab程序。 3.代码特点:参数化编程、参数可方便更改、代码编程思路清晰、注释明细。 4.适用对象:计算机,电子信息工程、数学等专业的大学生课程设计、期末大作业和毕业设计。
资源推荐
资源详情
资源评论
收起资源包目录
超极化磁共振成像matlab工具箱.zip (1082个子文件)
minpeakrf.c 13KB
abrx.c 3KB
b2a.code.c 3KB
cabc2rf.code.c 2KB
cabc2rf.c 2KB
b2rf.c 2KB
b2a.c 2KB
four1.c 956B
dynth01_phased.cmplx 4.5MB
Copyright_Information 2KB
E985S2I40.DCM 142KB
E985S2I77.DCM 142KB
E985S2I70.DCM 142KB
E985S2I39.DCM 142KB
E985S2I51.DCM 142KB
E985S2I76.DCM 142KB
E985S2I49.DCM 142KB
E985S2I53.DCM 142KB
E985S2I52.DCM 142KB
E985S2I55.DCM 142KB
E985S2I50.DCM 142KB
E985S2I61.DCM 142KB
E985S2I41.DCM 142KB
E985S2I78.DCM 142KB
E985S2I42.DCM 142KB
E985S2I71.DCM 142KB
E985S2I73.DCM 142KB
E985S2I57.DCM 142KB
E985S2I58.DCM 142KB
E985S2I46.DCM 142KB
E985S2I66.DCM 142KB
E985S2I59.DCM 142KB
E985S2I65.DCM 142KB
E985S2I48.DCM 142KB
E985S2I81.DCM 142KB
E985S2I56.DCM 142KB
E985S2I62.DCM 142KB
E985S2I79.DCM 142KB
E985S2I75.DCM 142KB
E985S2I45.DCM 142KB
E985S2I54.DCM 142KB
E985S2I80.DCM 142KB
E985S2I82.DCM 142KB
E985S2I60.DCM 142KB
E985S2I74.DCM 142KB
E985S2I69.DCM 142KB
E985S2I63.DCM 142KB
E985S2I43.DCM 142KB
E985S2I68.DCM 142KB
E985S2I67.DCM 142KB
E985S2I47.DCM 142KB
E985S2I3.DCM 142KB
E985S2I24.DCM 142KB
E985S2I17.DCM 142KB
E985S2I15.DCM 142KB
E985S2I11.DCM 142KB
E985S2I18.DCM 142KB
E985S2I13.DCM 142KB
E985S2I9.DCM 142KB
E985S2I27.DCM 142KB
E985S2I19.DCM 142KB
E985S2I35.DCM 142KB
E985S2I30.DCM 142KB
E985S2I21.DCM 142KB
E985S2I12.DCM 142KB
E985S2I72.DCM 142KB
E985S2I5.DCM 142KB
E985S2I31.DCM 142KB
E985S2I2.DCM 142KB
E985S2I34.DCM 142KB
E985S2I22.DCM 142KB
E985S2I28.DCM 142KB
E985S2I37.DCM 142KB
E985S2I26.DCM 142KB
E985S2I36.DCM 142KB
E985S2I10.DCM 142KB
E985S2I4.DCM 142KB
E985S2I32.DCM 142KB
E985S2I1.DCM 142KB
E985S2I14.DCM 142KB
E985S2I38.DCM 142KB
E985S2I33.DCM 142KB
E985S2I64.DCM 142KB
E985S2I84.DCM 142KB
E985S2I6.DCM 142KB
E985S2I83.DCM 142KB
E985S2I44.DCM 142KB
E985S2I23.DCM 142KB
E985S2I7.DCM 142KB
E985S2I25.DCM 142KB
E985S2I29.DCM 142KB
E985S2I8.DCM 142KB
E985S2I16.DCM 142KB
E985S2I20.DCM 142KB
E985S2I89.DCM 142KB
E985S2I91.DCM 142KB
E985S2I92.DCM 142KB
E985S2I90.DCM 142KB
E985S2I86.DCM 142KB
E985S2I87.DCM 142KB
共 1082 条
- 1
- 2
- 3
- 4
- 5
- 6
- 11
资源评论
Matlab科研辅导帮
- 粉丝: 1w+
- 资源: 7491
上传资源 快速赚钱
- 我的内容管理 展开
- 我的资源 快来上传第一个资源
- 我的收益 登录查看自己的收益
- 我的积分 登录查看自己的积分
- 我的C币 登录后查看C币余额
- 我的收藏
- 我的下载
- 下载帮助
安全验证
文档复制为VIP权益,开通VIP直接复制
信息提交成功