Multi-Scale Brain Parcellator

This pipeline is developed by the Hagmann’s group at the University Hospital of Lausanne (CHUV) for use within the SNF Sinergia Project 170873, as well as for open-source software distribution.

Digital Object Identifier (DOI) Continuous Integration Status Documentation Status


Multi-Scale Brain Parcellator, part of the Connectome Mapping Toolkit (CMTK), is a BIDS App that implements a full anatomical MRI processing pipeline, from raw T1w data to structural brain parcellation at five different scales.


The Multi-Scale Brain Parcellator pipelines uses a combination of tools from well-known software packages, including FSL, FreeSurfer, ANTs as well as in-house tools from CMTK.

This tool allows you to easily do the following:

  • Take T1 from raw to brain parcellations at 5 different scales.
  • Implement tools from different software packages.
  • Automate and parallelize processing steps, which provides a significant speed-up from typical linear, manual processing.

Reproducibility and replicatibility are promoted through the distribution of a BIDSApp, a software container image which provide a frozen environment where versions of all external softwares and libraries are fixed.


Work supported by the SNF Sinergia Grant 170873 (

License information

This software is distributed under the open-source license Modified BSD. See license for more details.

All trademarks referenced herein are property of their respective holders.

Copyright (C) 2009-2019, Brain Communication Pathways Sinergia Consortium, Switzerland.