Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping
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 mainly addresses all points raised by the JOSS review.
What's Changed
Updates
- Nipype has been updated from
1.7.0
to1.8.0
. (PR #184) See Nipype changelog) for more details.
Bug fix
- Add missing
cmp.stages.eeg
tosetup_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)
Name | Size | Download all |
---|---|---|
md5:8b55d74141e189aaef1ac3768afaa4eb
|
298.3 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/connectomicslab/connectomemapper3/tree/v3.0.4 (URL)