Scanner To Publication User Interface for ASL Imaging
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Table of Contents
This project wraps around ExploreASL to provide users with a friendly and modern interface for analyzing their arterial spin labeling datasets, including:
- Importing their ASL datasets into Brain Imaging Data Standard (BIDS) format
- Defining and re-using data parameters across studies for easier troubleshooting
- Adjusting BIDS-specific fields at the level of individual scans to cater to the specific needs of each dataset
- Running ExploreASL's modules in a parallel manner using multiprocessing to split the workload within and between studies
- Visualize and interact with the processed dataset using graphs that allow for loading in specific cerebral perfusion volumes when users click on datapoints
The latest downloadable releases for your operating system can be found here.
Complete documentation for this project is hosted on GitHub Pages. While it is recommended to give it a general read-through before using the application, most of the inputs within the application are accompanied by helper captions that provide additional information when completing a specific step.
Depending on the type of ExploreASL installation you have, you will need either:
- A standard MATLAB installation that preferrably at least R2019a and ExploreASL from GitHub. This is currently the more stable option.
OR
- MATLAB Runtime R2019a (9.6) and a pre-compiled version of ExploreASL (currently not publically available; please contact the developers of ExploreASL for more information)
Head on over to the Releases and download the appropriate version for your operating system
Just double-click the installer. The application will be silently installed in the background and will finish when a Desktop shortcut is created.
Open a terminal, change the current working directory to the location of the .deb file and type in:
sudo apt install ./exploreasl-gui_0.5.0_amd64.debWhere the version number within the filename may differ depending on the latest release.
The GUI will then be installed and a shortcut is automatically available from typing out exploreasl in your Super key search bar.
Open the .dmg file and drag the application to your Applications folder. The application will then be available from your Launchpad.
NOTE: The application is not signed, and in all likeliness you will receive an error message akin to the following the first time you run the application:
Click on Cancel and then go to your Security & Privacy settings. Under the General tab, click on "Open Anyway" to allow the application to run.
The second time you run the application, you will be prompted with a similar message, but this time you will be able to click on "Open" to run the application.
After this, you will be able to run the application without any issues and you will not be prompted with any more warning messages for subsequent attempts.
In your search bar, look for "Add or remove programs". Select the application and click uninstall.
Open a terminal and type in:
sudo apt remove exploreasl-guiGo to the Applications folder and drag & drop the ExploreASL-GUI.app application to the Trash bin.
Click here for more information on NodeJS installation.
Simply install it via the command line:
npm install --global yarn- Clone the repo using:
git clone https://github.com/MauricePasternak/ExploreASL-GUI.git
- Install Javascript packages contained within
package.jsonyarn install
- Start up the GUI with hot-reload and have a crack at it
yarn start
- If you'd like to package the application for your operating system:
yarn make
/---|
|-> assets (media such as icons)
|-> backend (logic executed by electron's IpcMain, i.e. spawning subprocesses to run ExploreASL)
|-> common -|
| |-> schemas (form validators & form schemas)
| |-> types (reusable types & typescript declarations)
| |-> utilityFunctions (reusable functions for reducing code use)
| |-> GLOBALS.ts (global variables used throughout)
|
|-> components (reuseable React components)
|-> ipc (logic for type-safe IpcMain <-> IpcRenderer communication)
|-> pages (non-reuseable React components that make up the pages of the GUI)
|-> stores (frontend-only collections of user-interface state)
... other files relate to project setup, package-handling, etc.
To start off with, you'll have to convert the output from your DICOM scanner(s) into proper Brain Imaging Data Structure (BIDS) format.
This is accomplished via a 4-step procedure:
- Define the pieces of information found in the folder names leading to the DICOM files (i.e. does a folder name contain the subject ID, the session ID, etc.)
- Define which folders account for which type of scan (i.e. ASL, T1w, T2w, etc.) and whether you'd like to have any visits/sessions renamed.
- Define how the various scans present with the dataset were acquired (see image below). This includes parameters like Post Labeling Delay, Background Suppression, etc.
- Run ExploreASL's Import Module.
Once a study has been imported to BIDS format, you can verify appropriate parameters are present for processing ASL by loading all BIDS sidecars into an interactive datagrid with built-in BIDS Validation (see below).
The datagrid allows for easy editing of BIDS fields with immediate feedback on whether the changes are valid or not. This is especially useful when dealing with anonymized datasets that lack certain fields.
There are a plethora of parameters tied to defining how an ASL-BIDS dataset should be processed. ExploreASL-GUI helps you define these parameters in a repeatable and reviewable manner.
Parameters are divided into 3 subsections:
- Study parameters (where is the study, what is its name, which subjects should be processed specifically, etc.)
- Modeling parameters (will a single or dual compartment model be used, what is the assumed T2* of the blood, etc.)
- ExploreASL pipeline parameters (which atlases to use when quantifying CBF ROIs, what should be the T-value for motion control, etc.)
Configurations can be easily saved with validation and re-loaded when tweaking settings.
ExploreASL-GUI allows for multiprocessing of several studies and/or several subjects per study in parallel, making the most of your computer's resources.
Percent completion, text feedback, and visual QC images of processed structural and functional images are provided while the pipeline is running (see below).
ExploreASL-GUI allows for streamlined QC analysis and overall visualization of the processed datasets. Users are given the ability to merge their own demographics/clinical/neuropsyche ancillary data with the CBF data generated by ExploreASL and represented as interactive graphs of 2 flavors:
- scatterplot (for continuous x continuous data; example below)
- swarmplot (for categorical x continuous data)
Emphasis on interactive. Clicking on datapoints will allow for the corresponding CBF volume to the loaded in for visual inspection across all dimensions and slices.
Plots with accompanying CBF volumes can be saved as PNGs for you publication purposes.
- Add Dark Mode.
- Add Image Feedback during processing.
- Support multiple ASL Import contexts.
- Create a Data Visualization Module.
- Add plot settings for plot legends (i.e. legend text fontsize, positioning, etc.) within the DataVisualization Module.
- Add more helpful information in the Process Studies module for when a study does not fully complete.
- Add help information on the steps within the Data Visualization Module.
- Add plot settings for renaming axis main labels within the Data Visualization Module.
- Add a separate module where users can pin-point change the JSON sidecars of individual subjects/visits/sessions.
- Allow for plots to be exported as PNG files in the Data Visualization Module.
- Migrate to Tauri for a more stable backend and better application performance, especially on Windows.
- Allow for the Data Visualization module to save/load a JSON parameters to allow for quick re-plotting.
- Add auto-update capability to the software so that users don't have to manually install new versions.
See the open issues for a full list of proposed features (and known issues).
Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.
If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!
- Fork the Project
- Create your Feature Branch (
git checkout -b feature/AmazingFeature) - Commit your Changes (
git commit -m 'Add some AmazingFeature') - Push to the Branch (
git push origin feature/AmazingFeature) - Open a Pull Request
Distributed under the MIT License. See LICENSE for more information.
Maurice Pasternak - maurice.pasternak@utoronto.ca
Project Link: https://github.com/MauricePasternak/ExploreASL-GUI
For GUI-related questions, please don't hesitate to drop an email at: maurice.pasternak@utoronto.ca
For more information on the main program, click on the following: CLICK ME!
For questions or concerns with the underlying ExploreASL program, the following individuals compromise the development team and may be contacted:
- Henk-Jan Mutsaerts; HenkJanMutsaerts@Gmail.com (ExploreASL creator)
- Jan Petr; j.petr@hzdr.de (ExploreASL creator)
- Michael Stritt; stritt.michael@gmail.com
- Paul Groot; p.f.c.groot@amsterdamumc.nl
- Pieter Vandemaele; pieter.vandemaele@gmail.com
- Maurice Pasternak; maurice.pasternak@utoronto.ca
- Luigi Lorenzini; l.lorenzini@amsterdamumc.nl
- Sandeep Ganji; Sandeep.g.bio@gmail.com