connectomicslab/connectomemapper3: Connectome Mapper v3.0.2 🧠🌍🌳✨
Creators
- 1. Department of Radiology, Lausanne University Hospital (CHUV), Switzerland
- 2. Departement des Neurosciences Cliniques, University of Geneva, Switzerland
- 3. Blue Brain Project, BBP-CORE, Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
- 4. Foxight, Geneva, Switzerland
Description
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()
forAnatomicalPipeline
,DiffusionPipeline
, andfMRIPipeline
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 theprocess()
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
, andfMRIPipeline
workflows are run with theMultiProc
plugin.
Bug fix
Major update of the
conda/environment.yml
andconda/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 -> 21.3.1numpy
: 1.19.2 -> 1.21.5matplotlib
: 3.2.2 -> 3.5.1traits
: 6.2.0 -> 6.3.2traitsui
: 7.0.0 -> 7.2.0graphviz
: 2.40.1 -> 2.50.0configparser
: 5.0.0 -> 5.2.0git-annex
: 8.20210127 -> 8.20211123pyside2
: 5.9.0a1 -> 5.13.2indexed_gzip
: 1.2.0 -> 1.6.4cvxpy
: 1.1.7 -> 1.1.18fsleyes
: 0.33.0 -> 1.3.3mrtrix3
: 3.0.2 -> 3.0.3duecredit
: 0.8.0 -> 0.9.1mne
: 0.20.7 -> 0.24.1datalad
: 0.14.0 -> 0.15.4datalad-container
: 1.1.2 -> 1.1.5statsmodels
: 0.11.1 -> 0.13.1networkx
: 2.4 -> 2.6.3pydicom
: 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
, andcmtklib.interfaces.diffusion
modules - Create and use a
.coveragerc
file to set the run ofCoverage.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
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
Files
connectomicslab/connectomemapper3-v3.0.2.zip
Files
(264.7 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/connectomicslab/connectomemapper3/tree/v3.0.2 (URL)