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Introduction to Pipeline
This documentation provides a step-by-step pipeline creation tutorial. We hope that it will be useful but understand there may be bugs or incompatibilities. Please remember to contact us if you find any bug with the documentation or an issue with the core plugin itself.
Dependencies
Matlab
Batch Context in its current format requires Matlab for the GUI portion. Most features of Batch Context are written with Octave compatibility in mind however. Batch Context is tested and working in the two version of Matlab we have available in our Lab. We however, will make an effort to support any newer version of Matlab, please make an issue in our repo if you find a bug and we also accept merge requests.
The versions we currently test with are
- Matlab 2012b
- Matlab 2015a
You only need Matlab for your local job submission and local job running.
Git
We require git to download our repos. If you would like to use another potentially simpler method you will have work that out on your own.
Getting git
Unix/Linux/MacOS
Git is usually available on Unix/Linux/MacOS by default, if you do not have git please consult your operating system documentation for assistance.
Windows
If you are using Windows you may use Git for Windows. You may also use a Linux/Unix/Posix compatibility layer such as Windows Subsystem for Linux (WSL) aka Bash on Ubuntu for Windows, Bash on Windows 10, or whatever marketing term they are using this week. Or you may also use git as a part of cygwin. We, however, will not support GUI based bash and will provide all documentation for git as it is on Linux.
EEGLAB
We support the newest stable version of EEGLAB, we will also accept Merge Requests for compatibility with future version of EEGLAB.
The newest version of EEGLAB can be obtained from the Swartz Center for Computational Neuroscience page.
Unpack into the Project Directory in the next step
Project Directory
Make a directory to house your project, this directory should be a self contained implementation of your pipeline.
We have provided a zip that starts you out with all the files we provided based on our experiences with our pipeline as well as the correct folder structure. You must install EEGLAB/Amica/Batch Context yourself.
tutorial_pipeline_template.zip
Suitable directory names should likely avoid spaces. We will use "tutorial_pipeline" for our example. Unpack the EEGLAB zip into tutorial_pipeline/dependencies/eeglab.
In our example the eeglab folder was eeglab7_1_3_13b we changed it to eeglab.
For now on all paths are relative to tutorial_pipeline.
Additionally, install amica in dependencies/eeglab/plugins/amica. Obtaining the file amica1.5.zip and unzipping it to the prior directory is sufficient in most cases.
If you are using Linux and have the Intel Fortran Compiler, Open MPI and GNU Make you can use our bundled version that has some helpful utilities. Read that repo for install instructions. Windows and MacOS users should use Jason Palmers versions (amica) from the link above.
Your directory should look something like this:
Editor Note: This image is out of date!
Install Batch Context
Using git
cd dependencies/eeg/plugins
git clone 'git@git.sharcnet.ca:bucanl_eeglab_extensions/batch_context.git'Or just download the zip from here and extract it into dependencies/eeg/plugins
Updated/Verified by Brad Kennedy on 2017-08-15