• Abstract
• Supported Pipelines
• Extensions
• Downloading this Package
• Updates, Git and Version Control
• Bug and Issues Tracking
• Contributing
• Contacting Us
  • Copywrite

Abstract

This repository contains a version of EEGLAB used for BUCANL specific pipelines. It is based off of the Octave compatible branch of the SCCN EEGLAB, but also contains additional extensions that are needed for the pipeline.

Supported Pipelines

This project will automatically be downloaded when you download any of the following BUCANL Pipelines:

• [bucanl_pipeline_asr_ amica] (https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica)

This project and can be found in the analysis/support/dependencies directory.

Extensions

This version of EEGLAB conftains the following BUCANL plugins as git sub modules:

• batch_context
• vised_marks
• interp_mont

as well as others found on the EEGLAB Extension Website including:

• clean_rawdata
• biosig
• ICMARC
• Prep
• HED Tools
• Fieldtrip

Downloading this Package

Pipeline
Git Repository

• https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica

git clone --recursive https://git.sharcnet.ca/bucanl_eeglab/eeglab_asr_amica.git  

The recursive command will download the sub modules that are need to run this pipeline.

Updates, Git and Version Control

You can determine if this version of EEGLAB is updated by checking through the website or by using git.
Even if your pipeline does not contain the most updated version of the associated BUCANL EEGLAB it should still work as designed, as we will only update the pipeline submoduals once they are ready. Also remember to use the recursive command when cloning the repository in order to get each of the sub modules.

Git

Navigate to your eeglab using the cd command. Using git status you will be able to see any new developments to sub modules in the untracked changes as (modified content) and yield something like this: This shows the changes that have happened in the sub modules.
You can also see that the current HEAD is listed at the top. If you are on the most updated version this will instead say master and no HEAD branch will appear. See git branch on one of the sub modules: In order to update a specific sub module you can:

cd /location/of/submodual            
checkout master 
git pull

or you can update all of the sub modules at once by preforming the following:

cd /location/of/eeglab          
git submodule foreach git pull

Website

Associated Pipelines
In order to determine which BUCANL EEGLAB version you are using navigate to the eeglab directory in the associated Pipeline Project.

You should see a brief code such as @2a691adf proceeding the EEGLAB link which is the version identifier. Proceed to the network tab of this EEGLAB project. You should see that the pipeline version code matches the start of the this EEGLAB version code.

Plugins
Very similarly you can navigate to the analysis/support/dependencies/eeglab/plugins directory you will see version identifiers for each of the BUCANL plugins. You can check to see if you have the most updated version of these plugins EEGLAB, but even if your EEGLAB does not contain the most updated version of the associated BUCANL Pipelines it should still work as designed.

Bug and Issues Tracking

We are using the built in Issue Tracker located here on git to keep track of any issues or bugs that users come across. We will be trying our best to keep an eye on these and work towards providing solutions.

To submit an ticket to the Issue Tracker navigate to the top of the page and click on Issues

Under this page click the green New Issue Button on the right side of the screen.

In the written section please provide a short but detailed description of the problem and attach any files that are necessary to replicate the issue.
Alternatively for remote jobs allow ** jdesjard** access to the Sharcnet folder containing the necessary files.

To give access cd to the folder containing the folder to be shared.

setfacl -Rm u:jdesjard:rwx fname

Where fname is the name of your file folder. To check that this worked use:

ls -l
getfacl fname

Where ls -l should show you a + before the file name, and getfacl fname will show all the users who can access the files contents.

Contributing

Contributing to this project is made easy with the git repository. If you would like to help contribute to this project please contact James Desjardins at the contact info below and we can look into getting your developing access . We are always look for ways to expand and improve our projects.

Contacting Us

If you have any questions or concerns about this project don't hesitate to contact us.

James Desjardins
High Performance Computing Consultant
SHARCNET, Compute/Calcul Ontario
Brock University
james.desjardins@computeontario.ca

Copywrite

Copyright (C) 2013 James Desjardins

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program (LICENSE.txt file in the root directory); if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

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