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 micapipe. The second is using the stand alone script micapipe_qc. Both options use the same optional arguments.

1micapipe -sub <subject_id> -out <outputDirectory> -bids <BIDS-directory> \

Optional arguments:

Optional argument


-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.

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

  • Red: Either incomplete or error

  • White: not processed

1micapipe -out <outputDirectory> -QC

Optional arguments:

There are no optional arguments for this command.