Virtual Scanner

Virtual Scanner: MRI on a Browser - Published in JOSS (2019)

https://github.com/imr-framework/virtual-scanner

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 2 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
✓
Committers with academic emails
2 of 10 committers (20.0%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

mri

Keywords from Contributors

mesh

Scientific Fields

Artificial Intelligence and Machine Learning Computer Science - 64% confidence

Computer Science Computer Science - 40% confidence

Neuroscience Life Sciences - 40% confidence

Last synced: 4 months ago · JSON representation

Repository

An end-to-end hybrid MR simulator/console

Basic Info

Host: GitHub
Owner: imr-framework
License: agpl-3.0
Language: Jupyter Notebook
Default Branch: master
Size: 145 MB

Statistics

Stars: 71
Watchers: 5
Forks: 21
Open Issues: 14
Releases: 2

Topics

mri

Created almost 7 years ago · Last pushed over 2 years ago

Metadata Files

Readme Contributing License Code of conduct

Virtual Scanner

Virtual Scanner is an end-to-end hybrid Magnetic Resonance Imaging (MRI) simulator/console designed to be zero-footprint, modular, and supported by open-source standards.

This project is a winning response to the ISMRM 2019 Junior Fellow Challenge (Africa), which poses the task of boosting accessibility to MRI training resources for underserved areas such as sub-Saharan Africa. We designed Virtual Scanner to help develop local expertise in these areas so that sustained deployment of MRI hardware is possible. Importantly, Virtual Scanner will be continually developed as a research tool that provides functionalities for simulating and prototyping MRI acquisition methods as well as services for sharing computational methods and resources with researchers around the world. Please read our publication in the journal of open source software here.

Virtual Scanner consists of two modes: in Standard Mode, a console-like GUI allows users to perform virtual scans and conduct basic analysis; in Advanced Mode, modular simulation/analysis of the entire signal chain may be performed.

Quick Start

If you just want to get started with using Virtual Scanner: 1. Install Python 3.6.x. 2. Create and activate a virtual environment of your choice. 3. In your terminal: pip install virtual-scanner, and finally, 4. In macOS, run the command: virtualscanner; in Windows, run this longer command within the main folder where you created your virtual environment: python Lib/site-packages/virtualscanner/coms/coms_ui/coms_server_flask.py

The browser application should have started running. To access the browser app, there are two ways: * Local hosting (only on the laptop running the script): go to the generated link (http://0.0.0.0:5000/) if you are a mac user, and this link (http://127.0.0.1:5000) if you are a windows user.
* Remote hosting : look up your IP address. Suppose it's 123.45.67.890, then you can go to (http://123.45.67.890:5000) to connect to the server remotely, either on the serving machine or different machines on the same network.

Now you can start playing with Virtual Scanner! Log in with your email address, select Standard or Advanced mode, and click "Begin Scan". Instructions for each tab are given in the Wiki.

Docker Start

This would be a good solution if you don't want to install the large number of dependencies to your host. We have tested Docker on Windows and Mac.

If you use a Windows 10 Pro system, first download Docker desktop and then run the following in the command line:

bash $ docker run -p 5000:5000 imrframework/virtual-scanner:latest

This downloads the pre-built image from Docker. You can then open up your browser to 127.0.0.1:5000 to see the interface.

If you use a Windows 10 Home system, please use an alternate approach (clone the repository or pip install) because Docker isn't supported on this system and we have not succeeded in using the image with Docker Toolbox.

If you use a Mac, you can either download the image as described above or you can locally build a Docker container to run the application in the following way:

First, build the container from the Dockerfile:

bash $ docker build -t virtualscanner .

Then you can run the container and bind port 5000 to expose the application to the host:

bash $ docker run -p 5000:5000 virtualscanner

And open up your browser to 0.0.0.0:5000to see the interface. The container is not intended for a production deployment, but rather is appropriate for local usage.

Pro Start

If you want to hack around with the code: 1. Install Python 3.6.x. 2. Create and activate a virtual environment of your choice. Here's a tutorial if you are using the PyCharm IDE, for example. 3. Clone the repo and cd into it. 4. pip install -e .. 5. Open the repo in your favourite IDE, hack around with the code. 6. Run virtualscanner/coms/coms_ui/coms_server_flask.py to run your changes.

Read the API documentation here and run the Python test scripts in each module with more options available than allowed on the GUI.

Standard Mode

The Register page allows you to choose a phantom for simulation. Its format is similar to the form for entering information of the subject when conducting real scans. Choose the "Numerical" phantom for all simulations now.

The Acquire page allows the user to choose either a Gradient Echo (GRE) or a Spin Echo (SE, with optional inversion recovery) sequence, enter the parameters, and simulate them on a cylindrical phantom ("Numerical") containing spheres with different T1, T2, and PD values.

The Analyze page allows the user to load a series of data acquired in ISMRM/NIST phantom for T1 or T2 mapping and conduct curve fitting to obtain T1 and T2 maps. In addition, it can detect spheres in the phantom, a feature useful for comparing generated parameter values to literature values.

Advanced Mode

The Tx (RF transmit) page allows one to calculate and plot SAR from pulseq .seq files. This feature is under development.

The Rx (RF receive) page allows one to visualize time-domain MR signal, generated from an arbitrary grayscale image, and see the effects of using different demodulation frequencies and ADC sampling rate. This feature is under development.

Other features, including phantom and sequence viewers and reconstruction methods, are in active development.

Known Issues

Please refer to the Known Issues document.

Contributing

If you would like to contribute to Virtual Scanner, please take a look at the Community Guidelines document.

Owner

Name: iMR Framework
Login: imr-framework
Kind: user
Location: New York

Repositories: 12
Profile: https://github.com/imr-framework

JOSS Publication

Virtual Scanner: MRI on a Browser

Published

November 25, 2019

DOI

10.21105/joss.01637

Volume 4, Issue 43, Page 1637