Connectome Mapper v3.0.4

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: v3.0.3...v3.0.4