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The main aim of the Computational Testing for Automated Preprocessing (CTAP) toolbox is to regularise and streamline EEG preprocessing, to minimise human subjectivity and error and facilitate easy batch processing for experts and novices alike. The main aim breaks down into two separate but complementary aims:
- batch processing using EEGLAB functions and
- testing and comparison of automated methodologies.
The CTAP toolbox provides two main functionalities to achieve these aims:
- the core supports scripted specification of an EEGLAB analysis pipeline and tools for running the pipe, making the workflow transparent and easy to control. Automated output of ‘quality control’ logs and imagery helps to keep track of what's going on.
- the testing module uses synthetic data to generate ground truth controlled tests of preprocessing methods, with capability to generate new synthetic data matching the parameters of the lab’s own data. This allows experimenters to select the best methods for their purpose, or developers to flexibly test and benchmark their novel methods.
Clone the GitHub repository to your machine using
git clone https://github.com/bwrc/ctap.git <dest dir>
Add the whole directory to your Matlab path. You also need to have EEGLAB added to your Matlab path.
A minimalistic working example can be found in
<dest dir>/ctap/templates/minimalistic_example/
Copy the cfg_minimal.m and pipebatch_minimal.m files and use them as a starting point for your own pipe.
More examples are available under <dest dir>/ctap/templates/.
The easiest way to use CTAP is by using the two template files provided: cfg_gettingstarted.m and pipebatch_gettingstarted.m. The cfg_gettingstarted.m file shows how to properly create the Cfg struct needed by CTAP. The pipebatch_gettingstarted.m shows how to specify an analysis pipe and how to execute it. For this simplistic case the measurement configuration file is automatically generated based on a directory with EEG files.
CTAP: this software package / repository
measurement configuration or MC: measurement configuration file contains a list of all test subjects, measurements and other relevant information needed to find the data files and to analyze them properly. This file can be automatically generated based on a directory with EEG data files or it can be custom made by the experienced user.
Configuration struct Cfg: A Matlab struct that contains all configurations that alter the behavior of CTAP, e.g. parameters to be passed to functions, path names to use for output, etc.