Connectome Mapper v3.0.3

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 mostly introduces the new pipeline dedicated to EEG modality with a tutorial, updates Freesurfer to 7.1.1, and adds a new tutorial that shows how to analyze the CMP3 connectomes.

What's Changed

New features

• CMP3 provides a new pipeline cmp.pipelines.functional.eeg.EEGPipeline dedicated to EEG modality with a collection of interfaces and methods implemented by the following modules: cmtklib.eeg, cmtklib.interfaces.eeg, cmtklib.interfaces.mne, and cmtklib.interfaces.pycartool.
  See PR #82 for more details.

Updates

• Freesurfer has been updated from 6.1.0 to 7.1.1. See PR #147 for more details.

Bug fix

• FIX: List of outputs are empty in inspector window of the parcellation and fmri_connectome stages.
  See PR #145 for more details.
• Correct way GM mask is generated and clean code in cmtklib/parcellation.py.
• Add interface to copy 001.mgz using hardlink.

Documentation

• Add documentation of new classes and functions introduced by the EEG pipeline.
• Add two ipython notebooks in docs/notebooks that are integrated directly in the docs with nbsphinx:
  • analysis_tutorial.ipynb: Show how to interact, analyze, and visualize CMP3 outputs.
  • EEG_pipeline_tutorial.ipynb: Show how to use the new API dedicated to the EEG pipeline.

Contributors

• Sebastien Tourbier
• Joan Rue Queralt
• Katharina Glomb
• Mikkel Schoettner

More...

Please check the main PR #146 page for more details.