FSL-pydocker tool

Overview

Due to the difficulty to install FSL in Windows OS, we created FSL-pydocker to simplify the execution of FSL command promt (FMRIB Software Library) within a Docker container. This tool facilitates the seamless integration of FSL into your workflow by providing a convenient command-line interface. By using FSL-pydocker you won't have problems to use FSL in Windows OS. This tool utilizes the brainlife/fsl Docker image.

Prerequisites

Before using FSL-pydocker, ensure that the following prerequisites are met:

• Python: Make sure you have Python installed on your system. ✅ (view appendix)

• Docker Engine: Ensure that Docker Engine is installed and active. ✅ (view appendix)

• requirements.txt: The project requires specific dependencies listed in the requirements.txt file. Install them using: ✅

    pip install -r requirements.txt
  

Usage

• First, download this repository or clone it:

      git clone https://github.com/adrialfonso/fsl-pydocker.git
  

• You need to link the specified local FSL volume path (with all your data) to the container's /volume/ directory (complete path). You can use the fsl-pydocker/volume/ directory as your default local volume path. In other words, you will need to move all your data (images and other stuff) to fsl-pydocker/volume:

  

• Remember that all the output will be stored in the same fsl-pydocker/volume/ directory. Open a "cmd" (Win+R and type "cmd"), navigate to your fsl-pydocker directory:

  

• And run the following command:

    python -m fsl-pydocker -v VOLUME_PATH
  

• IMPORTANT! VOLUME_PATH corresponds to your local fsl-pydocker/volume path, it is obligatory to indicate the absolute path (example: "C:\Users\XYZ\Desktop\fsl-pydocker\volume"). If the previous command doesn't work, try:

    python3 -m fsl-pydocker -v VOLUME_PATH
  

Contributing

• Feel free to contribute to the development of FSL-pydocker. Create a fork of the repository, make your changes, and submit a pull request.

Appendix

• Python: Make sure you have installed python 3+. If not, download it from python.org

• Docker Engine: Docker is an open source containerization technology for building and containerizing your applications. To be able to run FSL-pydocker in a Windows OS, you need to make sure that Docker Engine is running background. Youn can follow this easy tutorial from Docker Desktop Documentation. Remember that every time you want to run FSL-pydocker, Docker Engine needs to be running (just open Docker Desktop before using FSL-pydocker).

• In order to check that both installations were succesful, try:

      python --version && docker ps
  

• or:

      python3 --version && docker ps
  

If no errors displayed, all is OK!