Quality control¶

micapipe includes an integrated module for quality control of the outputs, which can be run at any point during processing. This step generates group and individual quality control reports, that will allow you to quickly identify missing files, verify registration performance, and check outputs requiring further inspection.

Individual QC¶

This module generates an individual html report with detailed information of each processing step, which can be used for rapid visualization of the processing status, core registrations, and data matrices by parcellation scheme and module.

There are two ways to run the individual quality control module, one is integrated within the main script mica-pipe. The second is using the stand alone script micapipe_qc. Both options use the same optional arguments.

mica-pipe -sub <subject_id> -out <outputDirectory> -bids <BIDS-directory> \
-QC_subj

Optional arguments:

Optional argument	Description
`-tracts` `<num>`	Number of streamlines used when computing the tractograms in `-SC` (default is 40M, where ‘M’ stands for millions, same as 40,000,000). If you used a different number of streamlines in your data processing, you should use this flag for the QC and input the same number of streamlines as you previously requested.
`-ses` `<num>` or `<str>`	Specify the session name with this flag (default: processing is performed as a single session).
`-tmpDir` `<path>`	Specify directory for temporary processing outputs.

micapipe_qc -sub <subject_id> -out <outputDirectory> -bids <BIDS-directory> \
-QC_subj

Optional arguments:

Additional flags can be specified when running the quality control using micapipe_qc

Optional argument	Description
`-tracts` `<num>`	Number of streamlines used when computing the tractograms in `-SC` (default is 40M, where ‘M’ stands for millions, same as 40,000,000). If you used a different number of streamlines in your data processing, you should use this flag for the QC and input the same number of streamlines as you previously requested.
`-ses` `<num>` or `<str>`	Specify the session name with this flag (default: processing is performed as a single session).
`-tmpDir` `<path>`	Specify directory for temporary processing outputs.
`-h` or `-help`	Print help with list of options
`-quiet`	Specify this flag to not print comments while processing
`-nocleanup`	When including this flag, the temporary directory will not be deleted at script completion
`-version`	Print software version

Directories created or populated by -QC_subj:

- <outputDirectory>/micapipe/<sub>/QC
- <outputDirectory>/micapipe/<sub>/QC/QC_png

Main output: <outputDirectory>/micapipe/<sub>/QC/<sub>_micapipe_qc.html

The subject QC html report contains different tabs, specifically one per module. Under each tab you can find:

Main inputs and outputs of each module
Main parameters of the processing steps (obtained from the json files)
Volume visualization of the main outputs
Visualization of the main registrations
Different surfaces generated by the pipeline
Atlas parcellations plotted on native surface
Structural connectome matrices
Functional connectome matrices
Geodesic distance matrices
Microstructural Intensity profiles and connectomes
Microstructural profiles (image intensities at each cortical depth) plotted on native surface

Group level QC¶

The group level quality control generates a report with all completed and processed modules by subjects. The report consists of a color coded table with rows as subjects and columns as the pipeline modules.

Blue: Completed
Orange: Either incomplete or error
Dark gray: not processed

1	mica-pipe -out <outputDirectory> -QC

Optional arguments:

There are no optional arguments for this command.

The QC table output by -QC can be found here:

Main output: <outputDirectory>/micapipe/micapipe_progress.html