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Published June 15, 2022 | Version v3.0.4
Software Open

Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping

  • 1. Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland
  • 2. Berlin Institute of Health at Charité; Department of Neurology with Experimental Neurology, Brain Simulation Section, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität 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 fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • 6. Foxight, Geneva, Switzerland

Description

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 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 version mainly addresses all points raised by the JOSS review.

What's Changed

Updates

Bug fix

  • Add missing cmp.stages.eeg to setup_pypi.py. (PR #166)
  • Add missing package data for parcellation in setup_pypi.py. (PR #182)
  • Use HTTPS instead of SSH for datalad clone in notebooks . (PR #181)
  • Add missing condition to handle custom BIDS files with session. (PR #183)
  • Integrate fix from Napari project for issues with menubar on Mac. (PR #174)
  • Use the most recent PyQt5 instead of PySide2 (older) for graphical backend of cmpbidsappmanager, which provides a fix to run Qt-based GUI on MacOSX Big Sur. (PR #188)

Documentation

  • Correct conda env create instruction in the README. (PR #164)
  • Refer to contributing guidelines in the README. (PR #167)
  • Use sphinx-copybutton extension in the docs. (PR #168)
  • Add notes about docker image and conda environment size and time to download. (PR #169)

JOSS paper

  • Integrate minor wording tweaks by @jsheunis. (PR #162)
  • Add higher level summary and rename the old summary to "Overview of Functionalities". (PR #175)

License

  • The license has been updated to a pure 3-clause BSD license to comply with JOSS. (PR #163)

Software development life cycle

  • Migrate ubuntu 16.04 (now deprecated) to 20.04 on CircleCI. (PR #172)

Contributors

More...

Full Changelog: https://github.com/connectomicslab/connectomemapper3/compare/v3.0.3...v3.0.4

Files

connectomicslab/connectomemapper3-v3.0.4.zip

Files (298.3 MB)

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