MSQMs: Magnetometers Quality Control Tool

MEG Signal Quality Metrics (MSQMs) is a fully automated quality control tool for OPM-MEG and SQUID-MEG.

Installation

pip install msqms

Using CLI Tool to Generate Summary Quality Control Reports

Command Description

The new msqms_summary command is used to generate summary quality control reports for multiple MEG files. This command automatically traverses all matching files in the specified directory.

Basic Usage

msqms_summary -i ./data -o ./reports -t opm

Parameter Explanation

• -i, --input: Input directory path (required, contains the directory with MEG files)
• -s, --suffix: File suffix (optional, default is '.fif', e.g., '.fif', '.ds')
• -o, --outdir: Output directory (required, default is the current directory)
• -t, --data_type: Data type (required, choices are 'opm' or 'squid')
• -n, --report_name: Summary report filename (optional, default is 'summary_report')
• -r, --recursive: Recursively search subdirectories (optional flag)

Usage Examples

Example 1: Process All .fif Files in the Directory (default)

msqms_summary -i ./data -o ./quality_reports -t opm

Example 2: Process Files with Specified Suffix

# Process .ds files
msqms_summary -i ./data -s .ds -o ./output -t squid

# Process .fif files (explicitly specified)
msqms_summary -i ./data -s .fif -o ./output -t opm

Example 3: Recursively Search Subdirectories

# Recursively search for all .fif files in subdirectories
msqms_summary -i ./data -r -o ./reports -t opm

Example 4: Custom Report Name

msqms_summary -i ./data -o ./output -t opm -n my_summary_report

Example 5: Complete Example

# Recursively search for all .fif files and generate a custom-named summary report
msqms_summary -i /path/to/meg/data -r -s .fif -o /path/to/output -t opm -n batch_quality_report

Output Files

After executing the command, the following will be generated:

1. Summary Report: {report_name}.html - Contains statistical information and visual charts for all files
2. Individual Reports: Each file will generate a corresponding {filename}.report.html
3. Visual Images: Each file will create a corresponding {filename}.imgs/ directory

Summary Report Features

The generated summary report includes:

• Summary Tab:

  • Summary statistics (total number of files, average scores, standard deviations, etc.)
  • MSQM score distribution charts
  • Distribution charts for various metrics (Time Metrics, Frequency Metrics, Entropy Metrics, Fractal Metrics, Artifacts)

• Individual Reports Tab:

  • A list of all files displaying filenames and scores
  • Clicking on any file allows viewing the detailed report below
  • Quality level badges (Excellent/Good/Fair/Poor/Bad)

Help Information

To view the complete help information:

msqms_summary --help

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Using CLI Tool to Generate Single Quality Control Report

Using msqms_report to Generate Quality Control (QC) Reports for MEG Data

Command Description

The msqms_report command is used to generate a Quality Control (QC) report for a specified MEG data file. This report includes various quality metrics calculated from the MEG data, such as signal quality, noise levels, and other key statistics. The report is saved in the specified output directory. Users must specify the type of MEG data, which can be either opm or squid.

Basic Usage

msqms_report -f ./auditory_raw.fif -o ./ -t opm

Parameter Explanation

• --file, -f:
  The path to the MEG file required for quality assessment. This option is mandatory.

• --outdir, -o:
  The directory where the generated quality report will be saved. This option is mandatory. Default is the current directory (.).

• --data_type, -t:
  The type of MEG data. Choose either opm or squid. This option is mandatory.

Usage Example

To generate a QC report for a data.fif file and save the report in the reports/ directory, use the following command:

msqms_report --file data/data.fif --outdir reports/ --data_type opm

This command processes the data.fif MEG file, calculates the relevant quality metrics for opm data, and generates an HTML quality control report in the reports/ directory. The generated report will be named data.report.html.

Help Information

To see the help documents for the command:

msqms_report -h

Bug reports

Please use the GitHub issue tracker to report bugs.

Interested in Contributing?

Please read our contributing guide.