Published June 7, 2024 | Version v3.2.0
Software Open

connectomicslab/connectomemapper3: Connectomemapper v3.2.0

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, 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 fixes some missing voxels in the ROIs of the parcellation Lausanne2018 (visible in insula for example) and integrate for multishell reconstruction MSMT-CSD (Issue #19 ) [[Jeurissen2014]] (https://mrtrix.readthedocs.io/en/dev/reference/references.html#jeurissen2014)

What's Changed

Updates

The conda environment files (conda/environment.yml ) for cmpbidsappmanager have been modified for packages update, as well as the environment.yml docker file (py38cmp-core).

Update expected outputs for circleci testing

New features

Multishell Reconstruction in diffusion has now the option to be perfomed with Dipy SHORE as in the previous versions or with multishell multissue with options for configuration files and/or cmpbidsappmanager: HARDI_singleTissue, HARDI_multiTissue, DSI, DTI (PR #234 ) Code refactoring

Contributors

Emeline Mullier

More...

Files

connectomicslab/connectomemapper3-v3.2.0.zip

Files (331.3 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/connectomicslab/connectomemapper3/tree/v3.2.0 (URL)