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 release introduces the capability to estimate carbon footprint of CMP3 execution and fix problems of conflicts during the creation of the conda environment. What's changed New features Allow the estimation of the carbon footprint while using the BIDS App python wrappers and the GUI. Estimations are conducted using codecarbon. All functions supporting this features have been implemented in the new module cmtklib.carbonfootprint. See PR #136 for more details. Code changes Creation of init_subject_derivatives_dirs() for AnatomicalPipeline, DiffusionPipeline, and fMRIPipeline that return the paths to Nipype and CMP derivatives folders of a given subject / session for a given pipeline. This removed all the implicated code from the process() method and improve modularity and readability. In the future, the different functions could be merged as there is a lot of code duplication between them. AnatomicalPipeline, DiffusionPipeline, and fMRIPipeline workflows are run with the MultiProc plugin. Bug fix Major update of the conda/environment.yml and conda/environment_macosx.yml to correct the problems of conflicts in the previous version, as reported in issue #137. This has resulted in the following package updates: pip: 20.1.1 -> 21.3.1 numpy: 1.19.2 -> 1.21.5 matplotlib: 3.2.2 -> 3.5.1 traits: 6.2.0 -> 6.3.2 traitsui: 7.0.0 -> 7.2.0 graphviz: 2.40.1 -> 2.50.0 configparser: 5.0.0 -> 5.2.0 git-annex: 8.20210127 -> 8.20211123 pyside2: 5.9.0a1 -> 5.13.2 indexed_gzip: 1.2.0 -> 1.6.4 cvxpy: 1.1.7 -> 1.1.18 fsleyes: 0.33.0 -> 1.3.3 mrtrix3: 3.0.2 -> 3.0.3 duecredit: 0.8.0 -> 0.9.1 mne: 0.20.7 -> 0.24.1 datalad: 0.14.0 -> 0.15.4 datalad-container: 1.1.2 -> 1.1.5 statsmodels: 0.11.1 -> 0.13.1 networkx: 2.4 -> 2.6.3 pydicom: 2.0.0 -> 2.2.2 See commit 483931f for more details. Documentation Add description of carbon footprint estimation feature. Improve description on how to use already computed Freesurfer derivatives. Misc Add bootstrap CSS and jquery JS as resources to cmtklib/data/report/carbonfootprint. They are used to display the carbon footprint report in the GUI. Clean the resources related to parcellation in cmtklib/data/parcellation and rename all files and mentions of lausanne2008 to lausanne2018. Removed unused cmtklib.interfaces.camino, cmtklib.interfaces.camino2trackvis, and cmtklib.interfaces.diffusion modules Create and use a .coveragerc file to set the run of Coverage.py with --concurrency=multiprocessing to be allow to track code inside Nipype interfaces, now managed by multiprocessing. Specify to Coverage.py with # pragma: no cover part of the code we know it won't be executed Code style Correct a number of code style issues with class names. Contributors Sebastien Tourbier Joan Rue Queralt More... Please check the main PR #140 page for more details. Full Changelog: https://github.com/connectomicslab/connectomemapper3/compare/v3.0.1...v3.0.2