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

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 to 1.8.0. (PR #184) See Nipype changelog) for more details. 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 Sebastien Tourbier J.S. (Stephan) Heunis More... Full Changelog: https://github.com/connectomicslab/connectomemapper3/compare/v3.0.3...v3.0.