Connectome Mapper v3.0.0 #131
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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 corresponds to the first offical release of Connectome Mapper 3 ! 🎄🎁✨
What's changed
New features
CMP3 can take custom segmentation (brain, white-matter, gray-matter and CSF masks, Freesurfer's aparcaseg - used for ACT for PFT) and parcellation files as long as they comply to BIDS Derivatives specifications, by providing the label value for the different entity in the filename. This has led to the creation of the new module
cmtklib.bids.io
, which provides different classes to represent the diversity of custom input BIDS-formatted files.(PR #88)
CMP3 generates generic label-index mapping
.tsv
files along with the parcellation files, in accordance to BIDS derivatives. This has led to the creation of the~cmtklib.bids.utils.CreateBIDSStandardParcellationLabelIndexMappingFile
and~cmtklib.bids.utils.CreateCMPParcellationNodeDescriptionFilesFromBIDSFile
interfaces, which allows us to create the BIDS label-index mapping file from the parcellation node description files employed by CMP3 (that includes\_FreeSurferColorLUT.txt
and\_dseg.graphml
), and vice versa.CMP3 provide python wrappers to the Docker and Singularity container images
connectomemapper3_docker
andconnectomemapper3_singularity
that generate and execute the appropriate command to run the BIDS App.(PR #109, PR #115, PR #130)
Major changes
.annot
files. This fixes the issue of overwritten labels encountered by in the process of creating the Lausanne2008 parcellation. Any code and data related to Lausanne2008 has been removed. If one still wish to use this old parcellation scheme, one should use CMP3v3.0.0-RC4
.Pipeline Improvements
Better handle of existing Freesurfer outputs. In this case, CMP3 does not re-create the
mri/orig/001.mgz
and connect the reconall interface anymore.Creation of 5TT, gray-matter / white-matter interface, and partial volume maps images are performed in the preprocessing stage of the diffusion pipeline only if necessary.
Output updates
Directories for the derivatives produced by cmp ([cmp]{.title-ref},
freesurfer
,nipype
were renamed tocmp-\<cmp_version>
,freesurfer-\<freesurfer_version>
, andnipype-\<nipype_version>
to comply with BIDS 1.4.0+. (PR #3 (fork))Code refactoring
Creation in
AnatomicalPipeline
,DiffusionPipeline
,fMRIPipeline
ofcreate_datagrabber_node()
andcreate_datasinker_node()
methods to reduce the code increate_workflow()
.The
run(command)
function ofcmp.bidsappmanager.core
has been moved tocmtklib.process
, which is used by the python wrappers incmp.cli
.Code Style
# fmt: off
and# fmt: on
tags.Documentation
Add instructions to use custom segmentation and parcellation files as inputs.
Add description in contributing page of format for code related to the connection of the nodes in a Nipype
Workflow
.Add instructions to use the python wrappers for running the BIDS App.
(PR #115)
Add notification about the removal of the old Lausanne2008 parcellation, and remove any other mentions in the documentation.
Software container
(PR #88)
Software development life cycle
Update the list of outputs of circleci tests with the new names of directories produced by cmp in
output_dir/
.Following major changes in the pricing plans of CircleCI but also to
improve its readability,
.circleci/config.yml
has beendramatically refactored, including:
(PR #88)
Contributors
Please check the main pull request 88 page for more details.
This discussion was created from the release Connectome Mapper v3.0.0.
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