connectomicslab/connectomemapper3: Connectome Mapper v3.1.0

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 the new pipeline dedicated to EEG modality and fixes a few bugs. 🤩

What's Changed

Updates

• The conda environment files (conda/environment.yml and conda/environment_macosx.yml) for cmpbidsappmanager have been greatly modified (PR #212).

• In all conda environment \*.yml and requirements.txt files, datalad and its container extension have been updated to version 0.17.2 and 1.1.6 respectively. (PR #209)

New features

• The new pipeline dedicated to EEG modality has been integrated into the BIDS App and cmpbidsappmanager. (PR #201 and PR #205)
• Option to apply or not band-pass filtering in fMRI pipeline. (PR #200)

Code refactoring

• Major refactoring of all the code related to the EEG pipeline. (PR #198)

Bug fix

• Problems to install and launch cmpbidsappmanager on Ubuntu. (PR #212)
• Fix nibabel to 3.2.2 as the imported functions of nibabel.trackvis has been moved since 4.0.0 and caused errors. (PR #211)
• Fix problem of traits not updated while making the diffusion pipeline config with ACT. (PR #200)

Documentation

• Update/add documentation for the EEG pipeline. (PR #208)

Software development life cycle

• Optimization of resources stored in the cache and in the workspace. (PR #201)
• Add tests 10 and 11 that run the EEG pipeline with the MNE and Cartool ESI workflow respectively. (PR #201)

Contributors

• Sebastien Tourbier

More...

Please check the main PR #149 page for more details.