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Published February 21, 2022 | Version v3.0.3
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connectomicslab/connectomemapper3: Connectome Mapper v3.0.3

Creators

  • 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 mostly introduces the new pipeline dedicated to EEG modality with a tutorial, updates Freesurfer to 7.1.1, and adds a new tutorial that shows how to analyze the CMP3 connectomes.

What's Changed

New features

  • CMP3 provides a new pipeline cmp.pipelines.functional.eeg.EEGPipeline dedicated to EEG modality with a collection of interfaces and methods implemented by the following modules: cmtklib.eeg, cmtklib.interfaces.eeg, cmtklib.interfaces.mne, and cmtklib.interfaces.pycartool. See PR #82 for more details.

Updates

  • Freesurfer has been updated from 6.1.0 to 7.1.1. See PR #147 for more details.

Bug fix

  • FIX: List of outputs are empty in inspector window of the parcellation and fmri_connectome stages. See PR #145 for more details.
  • Correct way GM mask is generated and clean code in cmtklib/parcellation.py.
  • Add interface to copy 001.mgz using hardlink.

Documentation

  • Add documentation of new classes and functions introduced by the EEG pipeline.
  • Add two ipython notebooks in docs/notebooks that are integrated directly in the docs with nbsphinx:
    • analysis_tutorial.ipynb: Show how to interact, analyze, and visualize CMP3 outputs.
    • EEG_pipeline_tutorial.ipynb: Show how to use the new API dedicated to the EEG pipeline.

Contributors

More...

Please check the main PR #146 page for more details.

Files

connectomicslab/connectomemapper3-v3.0.3.zip

Files (260.8 MB)

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Additional details

Related works

Is supplement to
https://github.com/connectomicslab/connectomemapper3/tree/v3.0.3 (URL)