Calculation Module (GUI)

Calculation Module (GUI)#

Thanks to the graphical user interface (GUI) you will be able to run MEGqc and generate reports without using the terminal. To open the GUI, click the MEGqc shortcut on your Desktop. Then the MEGqc GUI will open alongside a bash terminal.

(the terminal will display more detailed information about the on-going processes, but you can safely close it)

launchgui

GUI visual theme

Click the left-corner icon of the GUI to open a dropdown list with all available visual themes. This will only affect the visual display of the GUI. This list also includes themes with high-contrast options.

1. Basic parameters#

To run the calculation module you need the following basic parameters.

  • Data directory: you can paste the path to your dataset or click Browse to select the folder manually.

  • Subjects: you can write all to analyze every subject, or enter a specific ID (e.g., 009 for sub-009).

  • Jobs: Choose how many parallels jobs to use during the processing of your data. The default option is 1, but you can increase the speed of the processing by increasing the number of parallel Jobs.

mini-megqc-gui
How do I know the right amount of parallel Jobs?

  • MEGqc automatically detects and displays the number of cores (‘CPUs’) and the total available RAM (see the lower-corner of the GUI).

  • The Info button will give you personalized recommendations based on system memory.

  • You may also use -1 to use all available cores.

2. Settings#

The Setting tab allows you to customize your analysis.

settings-gui

The settings are grouped into categories:

  • The General group of settings allows you to select the channel types (mag or grad or both), and the specific metric to compute (e.g. STD, PSD or PTP). You can also apply your analysis to a smaller snippet of data by modifying data_crop_tmin and data_crop_tmax.

  • The Filtering and Epoching groups of settings allow you to edit how the filtering and epoching should be applied, such as high-pass / low-pass cut-offs frequencies and time windows.

  • Metric-specfic settings: every metric includes their own editable group of settings, such as how many standard deviations from the mean to use as a threshold, the edge frequencies for PSD calculation, or the minimun PTP amplitude to count as a peak.

When you hover over each editable parameter, you’ll see a short description along with the default value. Their default values were calculated by the ANCPLab to be compatible with a broad variety of datasets.

Once you have adjust your settings, don’t forget to click on the Save Settings button at the very end.

(if you want a detailed explanation of all the settings available, visit the settings page)


3. Run Calculation#

Once you’ve set your parameters (Data directory, Subjects and parallel Jobs) click Run Calculation. The Log window will display the ongoing process, including updates and any errors. You can also find more detailed information in the terminal window.

gui-log

“There are already config files used for this data set”#

If you have already processed the dataset, the terminal will ask you if you want to use again the same config files with the previous customized settings.

The terminal will display a numbered list of paths to previous config files used for the data set. Then it will ask you to Enter the number of the config file you want to use, or press Enter to use the default one.

  • Enter the corresponding number of the config file path you want to reuse. The terminal will ask you to confirm if you want to RERUN these subject with the same config parameters.

  • If you don’t want to use any previous config file, just press Enter to continue with your default setting

Warning

Rerun datasets, independently of the users’ decision over the settings, seems to be failing. The calculation doesn’t continue, the terminal becomes unresponsive.

Congratulations! You’ve successsfully run the calculation module! 🎉#

Once the process is finished, a new folder called MEG_qc will be created inside your dataset’s derivatives folder . This folder will contain one subfolder per subject, with machine-readable files (.tsv and .json) for each metric, run and task. If you’re following this tutorial, the path to the MEGqc derivatives might look like this:

/path/to/your/dataset/ds003483/derivatives/Meg_QC/calculation/sub-009/

Next section#

In the next section, you’ll learn how to use the calculation derivatives to generate the HTML reports with MEGqc’s plotting module.


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