Published October 25, 2022 | Version v3.1.0
Software Open

connectomicslab/connectomemapper3: Connectome Mapper v3.1.0

  • 1. Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland
  • 2. Berlin Institute of Health at CharitĂ©; Department of Neurology with Experimental Neurology, Brain Simulation Section, CharitĂ© UniversitĂ€tsmedizin Berlin, corporate member of Freie UniversitĂ€t Berlin and Humboldt-UniversitĂ€t zu Berlin, Berlin, Germany
  • 3. Department of Clinical Neurosciences, Division of Neurology, Geneva9 University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
  • 4. Departement des Neurosciences Cliniques, University of Geneva, Switzerland
  • 5. Blue Brain Project, École polytechnique fĂ©dĂ©rale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • 6. Foxight, Geneva, Switzerland


Connectome Mapper 3 implements, in accordance to the BIDS-App standard, full anatomical, diffusion, and resting/state functional MRI processing pipelines, from raw T1, DWI, BOLD, and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices, based on a new version of the Lausanne parcellation atlas (Cammoun et al, 2012), aka Lausanne2018.

This first minor version integrates the new pipeline dedicated to EEG modality and fixes a few bugs. đŸ€©

What's Changed


  • The conda environment files (conda/environment.yml and conda/environment_macosx.yml) for cmpbidsappmanager have been greatly modified (PR #212).

  • In all conda environment \*.yml and requirements.txt files, datalad and its container extension have been updated to version 0.17.2 and 1.1.6 respectively. (PR #209)

New features

  • The new pipeline dedicated to EEG modality has been integrated into the BIDS App and cmpbidsappmanager. (PR #201 and PR #205)
  • Option to apply or not band-pass filtering in fMRI pipeline. (PR #200)

Code refactoring

  • Major refactoring of all the code related to the EEG pipeline. (PR #198)

Bug fix

  • Problems to install and launch cmpbidsappmanager on Ubuntu. (PR #212)
  • Fix nibabel to 3.2.2 as the imported functions of nibabel.trackvis has been moved since 4.0.0 and caused errors. (PR #211)
  • Fix problem of traits not updated while making the diffusion pipeline config with ACT. (PR #200)


  • Update/add documentation for the EEG pipeline. (PR #208)

Software development life cycle

  • Optimization of resources stored in the cache and in the workspace. (PR #201)
  • Add tests 10 and 11 that run the EEG pipeline with the MNE and Cartool ESI workflow respectively. (PR #201)



Please check the main PR #149 page for more details.



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