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Connectome Mapper v3.1.0

25 Oct 13:51
@sebastientourbier sebastientourbier
v3.1.0
35cb2ee
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Connectome Mapper v3.1.0 Latest
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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, 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

More...

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

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Connectome Mapper v3.0.4

15 Jun 10:15
@sebastientourbier sebastientourbier
v3.0.4
2ce5619
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Connectome Mapper v3.0.4

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 mainly addresses all points raised by the JOSS review.

What's Changed

Updates

Bug fix

  • Add missing cmp.stages.eeg to setup_pypi.py. (PR #166)
  • Add missing package data for parcellation in setup_pypi.py. (PR #182)
  • Use HTTPS instead of SSH for datalad clone in notebooks . (PR #181)
  • Add missing condition to handle custom BIDS files with session. (PR #183)
  • Integrate fix from Napari project for issues with menubar on Mac. (PR #174)
  • Use the most recent PyQt5 instead of PySide2 (older) for graphical backend of cmpbidsappmanager, which provides a fix to run Qt-based GUI on MacOSX Big Sur. (PR #188)

Documentation

  • Correct conda env create instruction in the README. (PR #164)
  • Refer to contributing guidelines in the README. (PR #167)
  • Use sphinx-copybutton extension in the docs. (PR #168)
  • Add notes about docker image and conda environment size and time to download. (PR #169)

JOSS paper

  • Integrate minor wording tweaks by @jsheunis. (PR #162)
  • Add higher level summary and rename the old summary to "Overview of Functionalities". (PR #175)

License

  • The license has been updated to a pure 3-clause BSD license to comply with JOSS. (PR #163)

Software development life cycle

  • Migrate ubuntu 16.04 (now deprecated) to 20.04 on CircleCI. (PR #172)

Contributors

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Full Changelog: v3.0.3...v3.0.4

Contributors

jsheunis
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Connectome Mapper v3.0.3

21 Feb 20:40
@sebastientourbier sebastientourbier
v3.0.3
9a74f0a
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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

More...

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

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Connectome Mapper v3.0.2 🧠🌍🌳✨

31 Jan 14:54
@sebastientourbier sebastientourbier
v3.0.2
adbeb3a
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Connectome Mapper v3.0.2 🧠🌍🌳✨

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

More...

Please check the main PR #140 page for more details.

Full Changelog: v3.0.1...v3.0.2

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Connectome Mapper v3.0.1

05 Jan 11:07
@sebastientourbier sebastientourbier
v3.0.1
b79fc79
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Connectome Mapper v3.0.1

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 correspond to the second official version release, which is mostly a bug fix and code refactoring release that allows the python packages of Connectome Mapper 3 to be available on PyPI. It incorporates Pull Request #132 and includes the following changes.

What's changed

Bug fix (CI)

  • Rename the project name in setup.pyand setup_pypi.py from cmp to connectomemapper. The cmp project name was already existing on PyPI, that caused continuous integration on CircleCI to fail during the last v3.0.0 release, while uploading the python packages of CMP3 to PyPI.

Code refactoring

  • Make cmp.bidsappmanager.gui.py more lightweight by splitting the classes defined there in different files.
    (See Issue #129 for more discussion details)

  • Split the create_workflow() method of the RegistrationStage into the create_ants_workflow(), create_flirt_workflow(), and create_bbregister_workflow().
    (See Issue #95 for more discussion details)

Code style

  • Correct a number of code style issues with class names

Contributors

More...

Please check the main pull request 132 page for more details.

Best wishes for 2022!!! 🍾 🥳

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Connectome Mapper v3.0.0

24 Dec 20:28
@sebastientourbier sebastientourbier
v3.0.0
781b845
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Connectome Mapper v3.0.0

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 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 and connectomemapper3_singularity that generate and execute the appropriate command to run the BIDS App.
    (PR #109, PR #115, PR #130)

Major changes

  • Lausanne2018 parcellation has completely replaced the old Lausanne2008 parcellation. In brief, the new parcellation was introduced to provide (1) symmetry of labels between hemispheres, and (2) a more optimal generation of the volumetric parcellation images, that now are generated at once from .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 CMP3 v3.0.0-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 to cmp-<cmp_version>, freesurfer-<freesurfer_version>, and nipype-<nipype_version> to comply with BIDS 1.4.0+. (PR #3 (fork))

Code refactoring

  • Creation in AnatomicalPipeline, DiffusionPipeline, fMRIPipeline of create_datagrabber_node()and create_datasinker_node() methods to reduce the code in create_workflow().

  • The run(command) function of cmp.bidsappmanager.core has been moved to cmtklib.process, which is used by the python wrappers in cmp.cli.

Code Style

  • Clean code and remove a number of commented lines that are now obsolete. Code related to the connection of nodes in the Nipype [Workflow]{.title-ref} adopts a specific format and are protected from being reformatted by BLACK with the # 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

  • Define multiple build stages in Dockerfile, which can be run in parallel at build with BUILDKIT.
    (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 been
    dramatically refactored, including:

    • Use BUILDKIT in docker build to take advantage of the multi-stage build
    • Reordering and modularization of the tests:
      • tests 01-02 (Docker): anatomical pipeline for each parcellation scheme
      • tests 03-06 (Docker): diffusion pipeline for dipy/mrtrix deterministic/probabilistic tractography
      • tests 07-08 (Docker): fMRI pipeline for FLIRT and BBRegistration registrations
      • test 09 (Singularity): anatomical pipeline for Lausanne2018 scheme
    • Creation of commands for steps that are shared between jobs to reduce code duplication
      (PR #88)

Contributors

More

Please check the main pull request 88 page for more details.

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Connectome Mapper v3.0.0-RC4

07 Mar 19:28
@sebastientourbier sebastientourbier
v3.0.0-RC4
249e4e5
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Connectome Mapper v3.0.0-RC4

This is the fourth release candidate of Connectome Mapper (v3.0.0-RC4) which merges PR #74.

Complete list of changes with respect to previous v3.0.0-RC3:

  • MAINT: Set debug=False in methods of cmtklib/config.py (9 hours ago) - commit 249e4e5
  • DOC: Update release date in changes.rst and copyright year in readme [skip ci] (9 hours ago) - commit de1da17
  • Merge pull request #74 from connectomicslab/release/v3.0.0-RC4 (9 hours ago) - commit 31f1576
  • CI: Remove {{ file }} in send_codecov_report (2 days ago) - commit 4a78d49
  • CI: Add missing docker spec in send_codecov_report (2 days ago) - commit 0bb0a26
  • CI: Fix indentation error in config.yml (2 days ago) - commit 755b2a3
  • CI: Send reports to Codecov (2 days ago) - commit 23b4e51
  • CI: Send coverage report to codecov (2 days ago) - commit 26eca00
  • REF: Review BIDS naming to differentiate parcellation from different atlas and scale (2 days ago) - commit d6a82d8
  • TEST: Remove duplicated lines in list of outputs of test-08 [skip ci] (2 days ago) - commit f74f721
  • TEST: Re-enable check of outputs for all tests (1-8) (2 days ago) - commit 339a23d
  • CI: Update lists of outputs for tests 07 and 08 (3 days ago) - commit 75456e8
  • CI: Remove test-09 that was exactly the same than test-01 (3 days ago) - commits d093794 9ee13a7
  • DOC: Review header level in outputs.rst [skip ci] (3 days ago) - commit 0f3b68e
  • DOC: Update index.rst [skip ci] (3 days ago) - commit 4ade5c2
  • DOC: Update changes.rst [skip ci] (3 days ago) - commits 3361395 cf522f2 adae02a 3fe0d4a a842f90 cd42a09
  • UPD: Update dataset_description.json of derivatives to conform to BIDS 1.4.0 (3 days ago) - commit 449d9f6
  • DOC: Review layout in outputs.rst [skip ci] (3 days ago) - commit eff219d
  • DOC: Update outputs.rst with new BIDS naming convention [skip ci] (3 days ago) - commit 02b093e
  • DOC: Review docstrings in files for pipelines (3 days ago) - commit 466fdcd
  • FIX: Remove debug option from check_input of fmri pipeline (3 days ago) - commit 1111ac9
  • DEL: Remove obsolete Check_Input_Notifications classes (3 days ago) - commit 0fa37bb
  • CI: Updated the list of outputs for all tests except for fmri (tests 7 and 8) (3 days ago) - commit 9204cb3
  • FIX: Correct typos (4 days ago) - commit bb72833
  • TEST: Commented all test for output differences in circleci config (4 days ago) - commit 740ed90
  • REF: Review BIDS naming using atlas as keyword type and use res-scale to differentiate scales (4 days ago) - commit 5ab54f0
  • FIX: Correct typos in substitution in the datasinker of fmri pipeline (4 days ago) - commit 6e8c3ab
  • DEL: Remove old commented code in fMRI.py (4 days ago) - commit c903395
  • MAINT: Review code to use pyside2 (GUI) (4 days ago) - commit 62f3ef3
  • DOCKER: Update to ubuntu:xenial-20210114 for FSL5.0 (5 days ago) - commits 19b7c86 3037a8e
  • DOCKER: Move installation of perl in first run (5 days ago) - commit 4e9e6b6
  • DOCKER: Update to ubuntu 18.04 (5 days ago) - commit cfc032d
  • DOCKER: Install perl to make freesurfer hippo and subfields happy (5 days ago) - commit 56c9a1e
  • UPD: Update to use pyside2 (qt) (5 days ago) - commit cbc9b60
  • DOC: Update installation.rst with a note on how to update CMP3 (5 days ago) - commit 5d29b70
  • DOC: Update changes.rst (5 days ago) - commit 866fbc3
  • STY: Correct remaining code style issues (5 days ago) - commit 22bd03e
  • FIX: Better handle float as string for ants_precision_type (6 days ago) - commit fc65400
  • FIX: Better handle float as string for ants_precision_type (6 days ago) - commit 7ceb98e
  • DEBUG: Set debug=True in set_pipeline_attributes_from_config() (6 days ago) - commit 58f11b9
  • FIX: Better handle float as string for ants_precision_type (6 days ago) - commit 5d91110
  • DEBUG: Set debug=True in save_configparser_as_json() (6 days ago) - commit 9c3046f
  • MAINT: Clean code and prints in connectomemapper3 script (6 days ago) - commit 380fedc
  • MAINT: Clean print in define_inspect_outputs() of fmriconnectome stage (6 days ago) - commit 3933c9b
  • MAINT: Clean code and prints in define_inspect_outputs() for all stages (6 days ago) - commit b9644ea
  • MAINT: Remove old commented code and review code layout in run.py (6 days ago) - commit f9fe9f5
  • REF: Creation of sub-methods to modularize clean_cache and reduce duplication (6 days ago) - commit b4ad67d
  • CI: Show python version in the docker image used in build-docker on circleci (6 days ago) - commit 9b3d5cc
  • FIX: Remove fstring for copyright to make python on circleci happy (6 days ago) - commit c30d8f7
  • MAINT: Review output generated by BIDS App in run.py (9 days ago) - commit 941a981
  • MAINT: Clean output print at loading of the GUI (9 days ago) - commit c9e6950
  • MAINT: Clean output print for copyright and config save/load methods (9 days ago) - commit a3e8190
  • MAINT: Clean output print and disable debug mode for config save/load methods (9 days ago) - commit e26627a
  • ENH: Remove log_visualization and circular_layout from configuration file (9 days ago) - commit c1d8b35
  • MAINT: Clean output print (9 days ago) - commit be0f0c9
  • MAINT: Review prints in config load/save (9 days ago) - commit 8ef9c2e
  • FIX: Review loading of dict from json (9 days ago) - commit 93e9713
  • FIX: Review conversion from init to json (9 days ago) - commit 8037195
  • FIX: Handle the loading of config parameters (9 days ago) - commit 33890ee
  • FIX: Handle differently tuple in the loading of config parameters (9 days ago) - commit a17b080
  • FIX: Save differently dict type of config parameters (9 days ago) - commit 8702682
  • FIX: Handle differently tuple in the loading of config parameters (9 days ago) - commit dafda7d
  • FIX: Handle differently list in the loading of config parameters (9 days ago) - commit 9db2c0b
  • FIX: Remove list to be handled in the loading of configuration parameter types (9 days ago) - commit 2075e61
  • MAINT: Review info message printed at launch of cmpbidsappmanager (9 days ago) - commit 00a32b5
  • MAINT: Review info message printed at launch of cmpbidsappmanager (9 days ago) - commit abe74b9
  • MAINT: Update main copyright line layout (9 days ago) - commit 0e62eff
  • MAINT: Review cmpbidsappmanager and try to use qt (pyside2) (9 days ago) - commit 8c1f4c2
  • MAINT: Review all print output generated by the GUI (9 days ago) - commit 3a34b82
  • MAINT: Remove obsolete methods and add debug mode for extra prints in cmtklib.util.py (9 days ago) - commit 7855b81
  • WIP: Better handle loading of configuration parameter types (9 days ago) - commits 10d8b7c d8f0b38 f5b394e 9bd70a5 26dbd5b fb9b722 fc6f6e7 36976ec 8f2e679 cf2fb4f 4b3ef59 18c0a05 da78108
  • FIX: Error in creating docker image caused by dbus with python2.7 (10 days ago) - commit 259f1cf
  • DEL: Remove a number of files now obsolete (10 days ago) - commit 97beaba
  • DOC: Update copyright (10 days ago) - commit 407d5d1
  • DOC: Update footer with special authors/version/copyright section (10 days ago) - commit 84e0a42
  • FIX: Remove cmp/bidsappmanager from .dockerignore (10 days ago) - commit 02721d2
  • FIX: Set cache for eggs before pip install (10 days ago) - commit 69ce438
  • DOC: Improve runonhpc.rst (10 days ago) - commit fab2bf6
  • DOC: Double the \ in commands of runonhpc.rst (10 days ago) - commit 2ee17cb
  • DOC: Improve command rendering in runonhpc.rst (10 days ago) - commit 7ab385c
  • DOC: Improve installation.rst (10 days ago) - commit b23cd15
  • DOC: Edit installation.rst (10 days ago) - commit 94c8237
  • DOC: Edits in tutorials (10 days ago) - commit bc84b13
  • DOC: Add prerequisites section to tutorials (10 days ago) - commit 90e7ec3
  • REF: Rename ubuntu16.04 to docker and related changes in Dockerfile (10 days ago) - commit 6ab48e5
  • DEL: Remove files related to obsolete main docker image (10 days ago) - commit 531ddf5
  • CI: Deleted run task related to removed setup_cmp.py (10 days ago) - commit ac57b6b
  • ENH: Merge the two setup files into one to make pip happy (10 days ago) - commit c0d76e5
  • WIP: Review how to retrieve parameters of anatomical pipeline (11 days ago) - commit d8d49a8
  • FIX: Review how to retrieve parameters of anatomical pipeline (11 days ago) - commit 88cb5e5
  • FIX: Create folder with right permissions and set PYTHON_EGG_CACHE in Dockerfile (11 days ago) - commit 2aeb6ca
  • ENH: Convert auto config files (INI) to JSON with cmpbidsappmanager (11 days ago) - commit eb30d03
  • MAINT: Set debug to False in cmtklib.config methods (11 days ago) - commit 3d20fc0
  • MAINT: Add extra blank line at the file end (11 days ago) - commit 8a95c43
  • MAINT: Edit a number of print outputs of cmpbidsappmanager and config (11 days ago) - commit 3b47bdb
  • WIP: Review how existing JSON file are loaded and saved (11 days ago) - commits 283e844 7045924
  • FIX: Add "none" to Enum for slice_timing in fmri_preprocessing stage (11 days ago) - commit b0ac394
  • FIX: Review how existing JSON file are loaded and saved (11 days ago) - commit a58aa10 d19004a 16e8875 f1e4295 9d544f3 a4125c3 6ad9e4b d531b68 3b661b4 f116a7e
  • ENH: Skip "_editor" attributes of stages in saved config (11 days ago) - commit 59d1afe
  • MAINT: Remove comments for freesurfer reconall node and set freesurfer_args to "" (11 days ago) - commit 51c929f
  • MAINT: Remove option to specify custom segmentations (11 days ago) - commit f927b90
  • DEBUG: Add additional debug prints in cmtklib/config.py (11 days ago) - commit 294fe0f
  • MAINT: Clean more prints generated by the config functions and the GUI (11 days ago) - commit 0ade58d
  • ENH: Use the new color print methods (11 days ago) - commit 8e0be3d
  • MAINT: Clean code and improve code style (11 days ago) - commit ef5582e
  • MAINT: Set debug argument to False when starting cmpbidsappmanager (11 days ago) - commit 6d649aa
  • MAINT: Rename package names in imports for pipelines in bidsappmanager/project.py (11 days ago) - com...
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Assets 2

Connectome Mapper v3.0.0-RC3

05 Feb 12:48
@sebastientourbier sebastientourbier
v3.0.0-RC3
34ae80f
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Connectome Mapper v3.0.0-RC3

This is the third release candidate of Connectome Mapper (v3.0.0-RC3) which merges PR #62.

Complete list of changes with respect to previous v3.0.0-RC2-patch1:

  • Merge pull request #62 from connectomicslab/v3.0.0-RC3 (4 minutes ago) - commit 34ae80f

  • DOC: update release date in changes.rst [skip ci] (7 minutes ago) - commit 07baaf8

  • DOC: Update usage and version in README [skip ci] (8 minutes ago) - commit 2a07d54

  • DOC: update copyright [skip ci] (8 minutes ago) - commit 1e1916b

  • CI: push singularity image of release as latest TAG [skip ci] (3 hours ago) - commit d3f1062

  • DOC: corrected link to section Nipype outputs [skip ci] (3 hours ago) - commit 4f5ae91

  • DOC: add description of BIDS entities employed in CMP outputs [skip ci] (3 hours ago) - commit 6366cae

  • DOC: review Nipype section in bidsappmanager and add link to outputs for more details [skip ci] (4 hours ago) - commit 41415a1

  • DOC: correct code style issues with lists not properly rendered [skip ci] (4 hours ago) - commit 35aa6ca

  • DOC: update description of --number_of_threads parser argument [skip ci] (4 hours ago) - commit 9ba43cd

  • DOC: correct style issue [skip ci] (4 hours ago) - commit 2fd5b23

  • MAINT: clean Dockerfile (25 hours ago) - commit 58517aa

  • CI: add expected output list for tests 7, 8 and 9 and enable difference check (27 hours ago) - commit 43d0e92

  • DOC: update changes.rst (27 hours ago) - commit 6556007

  • Merge branch 'master' (v3.0.0-RC2-patch1) into v3.0.0-RC3 (28 hours ago) - commit 4eb3e6f

  • MAINT: removed commented lines (coverage-reporter) in .circleci/config.yml (2 days ago) - commit 0e4ae16

  • CI: Use manually Codacy Coverage Reporter (2 days ago) - commit c75d899

  • CI: remove deployment of latest tag image on singularity for space (3 days ago) - commit 08c4eb9

  • CI: clean codacy_coverage_report job (7 days ago) - commit a9aa57c

  • MAINT: update codacy-reporter circleci orb (7 days ago) - commit c5c4c03

  • FIX: try to set MKL_NUM_THREADS=1 and OMP_NUM_THREADS=1 in Dockerfile (8 days ago) - commit 3e76e5c

  • MAINT: revert to use dipy.tracking.utils.seeds_from_mask() (8 days ago) - commit 3b1804c

  • FIX: reviewed multithreading management to set only number of threads for Freesurfer and ANTs (8 days ago) - commit 80563b2

  • MAINT: reviewed print with fstring and correct comment style issues (8 days ago) - commit 256913a

  • FIX: typo in run.py (8 days ago) - commit 6a5166a

  • FIX: install and use threadpoolctl to limit the number of OpenMP threads used by Numpy (8 days ago) - commit 8848498

  • DEL: remove installation of threadpoolctl (8 days ago) - commit bb6437d

  • FIX: try to use dipy to set omp num threads (8 days ago) - commit d01a43b

  • FIX: install and use threadpoolctl to limit the number of OpenMP threads used by Numpy (8 days ago) - commit bd7730d

  • MAINT: remove os.environ.update(MKL_NUM_THREADS='1') in run.py (8 days ago) - commit d5162ec

  • FIX: set OMP_NUM_THREADS to 1 prior to dipy.utils.seeds_from_mask (8 days ago) - commit 72fa6b3

  • FIX: set MK_NUM_THREADS to 1 to make numpy.dot working ? (9 days ago) - commit 24844d2

  • FIX: review how to set OMP_NUM_THREADS (9 days ago) - commit da07fa1

  • DOC: correct description of number_of_threads in docstring (9 days ago) - commit b994d7d

  • MAINT: remove old implementation commented (9 days ago) - commit 267958d

  • FIX: move first "import numpy" after setting the multi-threading variables (9 days ago) - commit a14df63

  • DEBUG: changed print() to IFLOGGER.info() (9 days ago) - commit 1396c0f

  • FIX: make sure seeds array is int (in interfaces/dipy.py / seeds_from_mask()) (11 days ago) - commit aa14b2c

  • FIX: update numpy (11 days ago) - commit 5e10bee

  • DEBUG: add prints in seeds_from_mask() (11 days ago) - commit 2771c1d

  • FIX: PeaksAndMetrics.shm_coeff w.r.t Dipy 1.3.0 (2 weeks ago) - commit 8af0a50

  • MAINT: use internal seeds_from_mask() in DirectionGetterTractography (2 weeks ago) - commit 27adab3

  • FIX: update estimation of response for CSD following major changes in Dipy 1.X (2 weeks ago) - commit 7f78dc7

  • DEBUG: insert dipy code for seeds_from_mask (2 weeks ago) - commit f597807

  • FIX: give vector of seed densities to dipy seeds_from_mask() (2 weeks ago) - commit 7804d67

  • FIX: test to remove clipMask as dipy seeds_from_mask() is triggering Segmentation Fault (l. 438) (2 weeks ago) - commit 15c486c

  • CI: add tests using the new config files in config.yml (2 weeks ago) - commit 2580992

  • CI: add fMRI config for testing FSL FLIRT, global nuisance regression, linear detrending and scrubbing (2 weeks ago) - commit f5a5b19

  • CI: add diffusion config for testing FLIRT co-registration and tractogram filtering with MRtrix3 SIFT (2 weeks ago) - commit 52a53ad

  • MAINT: reviewed code layout and prints with f-string in dipy.py (2 weeks ago) - commit fb04560

  • UPD: reverted back to ANTs 2.2.0 and reviewed comment style (2 weeks ago) - commit 9567877

  • MAINT: code style (2 weeks ago) - commit be114f3

  • UPD: update interface in dipy.py for EudXTracking with Tensor model w.r.t major Dipy 1.X changes (2 weeks ago) - commit 7b5bede

  • FIX: uncommented debug option and set debug to False for dwibiascorrect (2 weeks ago) - commit 3b79536

  • FIX: comment debug option in mrtrix dwibiascorrect that was raising errors after update to mrtrix 3.0.2 (2 weeks ago) - commit a156bd9

  • DOC: correct typo in docstring (2 weeks ago) - commit 48196a3

  • MAINT: add {} in environment variables with underscores (2 weeks ago) - commit b1b5f3c

  • Merge remote-tracking branch 'origin/v3.0.0-RC3' into v3.0.0-RC3 (2 weeks ago) - commit 9136f16

  • DOC: corrected typos and image in the BIDS App execution window (2 weeks ago) - commit fe6cf8f

  • FIX: review denoising/biasfieldcorrection node connection in preprocessing.py (2 weeks ago) - commit 0b3e3e8

  • FIX: update ANTs to 2.3.1 (2 weeks ago) - commit ad5f054

  • DOC: add the new images used in bidsappmanager.rst [skip ci] (3 weeks ago) - commit fa79ec0

  • DOC: updated images in bidsappmanager.rst [skip ci] (3 weeks ago) - commit 945dbfc

  • UPD: update dwibiascorrect command following change in mrtrix 3.0.2 (3 weeks ago) - commit e0b6569

  • DOC: updated instructions in bidsappmanager.rst [skip ci] (3 weeks ago) - commit 224ae31

  • DOC: correct conda activate command in bidsappmanager.rst [skip ci] (3 weeks ago) - commit 3739d82

  • FIX: unterminated quoted string error raised by CI (3 weeks ago) - commit f04b9d1

  • MAINT: reviewed installation of networkx (3 weeks ago) - commit 6072e30

  • REFACT: install mrtrix3 using conda (3 weeks ago) - commit 669c45e

  • UPD: update mrtrix to 3.0.2 in dockerfile (3 weeks ago) - commit 22d1d7e

  • UPD: update conda env with Nipype 1.5.1 (3 weeks ago) - commit c36d3d8

  • UPD: update conda env with dipy 1.3.0 and cvxpy 1.1.7 (3 weeks ago) - commit be9da76

  • MAINT: clean BIDSApp entrypoint script run_cmp3.sh [skip ci] (3 weeks ago) - commit 7d0ed0b

  • VERSION: update to v3.0.0-RC3 (3 weeks ago) - commit e66cc4d

  • STYLE: improved code style for connectomemapper3 cmd generation (3 weeks ago) - commit 562afbd

  • ENH: add color for warning and error prints during BIDS App settings check [skip ci] (3 weeks ago) - commit 9962617

  • FIX: print new attributes relative to RNG and ITK threads during BIDS App setting check [skip ci] (3 weeks ago) - commit 16bfa58

  • MAINT: use fstring to print summary of BIDS App settings check [skip ci] (3 weeks ago) - commit 0b7d42f

  • MAINT: correct code style [skip ci] (3 weeks ago) - commit 6edcf5c

  • DOC: add link to git-annex install page [skip ci] (3 weeks ago) - commit 20aab0d

  • DOC: add note to checkout the master branch if bugs in the GUI were fixed after version release [skip ci] (3 weeks ago) - commit 9119b84

  • DOC: updated installation instructions of conda environment on Mac [skip ci] (3 weeks ago) - commit 3fb0d50

  • ENH: add conda environment for macosx where git-annex has been removed (3 weeks ago) - commit 3cdee53

    Auto-generated with

    git log v3.0.0-RC2-patch1..HEAD --pretty=format:' * %s %Cgreen(%cr) - commit %Cred%h%Creset' --abbrev-commit

Summary of changes is available at the documentation.

Assets 3

Connectome Mapper v3.0.0-RC2-patch1

04 Feb 08:24
@sebastientourbier sebastientourbier
v3.0.0-RC2-patch1
baad58a
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Connectome Mapper v3.0.0-RC2-patch1

This version fixes bugs in the second release candidate of Connectome Mapper 3 (v3.0.0-RC2).
In particular, it includes:

Bug fixes

  • Fix the error to save connectome in GraphML format reported in #65 (PR #66).

Software development life cycle

  • Remove publication of the Singularity image to sylabs.io when the master branch is updated for the sake of space (11GB limit)

Commits

  • CI: remove publication of latest tag image on sylabs.io for space (2 days ago) - commit c765f79
  • Merge pull request #66 from connectomicslab/v3.0.0-RC2-hotfix1 (3 days ago) - commit 0a2603e
  • FIX: update g2.node to g2.nodes when saving connectomes as graphml (fix #65) (6 days ago) - commit d629eef
  • FIX: enabled/disabled gray-out button "Run BIDS App" with Qt Style sheet [skip ci] (3 weeks ago) - commit 10e78d9
  • MAINT: removed commented lines in cmpbidsappmanager/gui.py [skip ci] (3 weeks ago) - commit 4cc11e7
  • FIX: check availability of modalities in the BIDS App manager window [skip ci] (3 weeks ago) - commit 80fbee2
  • MAINT: update copyright year [skip ci] (3 weeks ago) - commit f7d0ffb
  • CI: delete previous container with latest TAG on sylabs.io [skip ci] (4 weeks ago) - commit 15c9b18
  • DOC: update tag to latest in runonhpc.rst [skip ci] (4 weeks ago) - commit 3165bcc
  • CI: comment lines related to version for singularity push (4 weeks ago) - commit 3952d46
Assets 2

Connectome Mapper v3.0.0-RC2

25 Dec 11:57
@sebastientourbier sebastientourbier
v3.0.0-RC2
7bbac75
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Connectome Mapper v3.0.0-RC2

This is the second release candidate v3.0.0-RC2 of Connectome Mapper which merges PR #45.

Summary of changes is available at the documentation.

Complete list of changes with respect to previous 3.0.0-RC1:

  • CI: fix double to single quotes in deploy_singularity_release [skip ci] (2 minutes ago) - commit 7bbac75
  • Merge remote-tracking branch 'origin/master' [skip ci] (3 hours ago) - commit 237596b
  • VERSION: update release date in cmp/info.py [skip ci] (3 hours ago) - commit 5c0069c
  • DOC: update docker command in README [skip ci] (3 hours ago) - commit d262303
  • CI: update creation of singularity token for deploy_singularity (5 hours ago) - commit 818f3f5
  • Merge pull request #45 from connectomicslab/v3.0.0-RC2-dev (5 hours ago) - commit d9135ac
  • Merge pull request #58 from connectomicslab/57_documentation_v3.0.0-RC2-dev [skip ci] (5 hours ago) - commit cc47e0e
  • DOC: update description of new options in changes.rst [skip ci] (5 hours ago) - commit d1a3799
  • DOC: update release date in changes.rst [skip ci] (5 hours ago) - commit 8ff2b3a
  • DOC: fix sphinx version that might fix correct rendering of figures in PDF [skip ci] (5 hours ago) - commit f3769cb
  • DOC: update link to https://sylabs.io/ in usage.rst [skip ci] (6 hours ago) - commit 1f092bc
  • DOC: review indent of singularity run example [skip ci] (6 hours ago) - commit 762299c
  • DOC: update references [skip ci] (6 hours ago) - commit 323a36e
  • DOC: update runonhpc.rst [skip ci] (6 hours ago) - commit 18e797c
  • DOC: rename page for api_doc [skip ci] (6 hours ago) - commit 5405c4f
  • DOC: update runonhpc.rst [skip ci] (6 hours ago) - commit 590306e
  • Merge branch 'v3.0.0-RC2-dev' into 57_documentation_v3.0.0-RC2-dev [skip ci] (7 hours ago) - commit 2c586eb
  • DOC: update doc about singularity and datalad [skip ci] (7 hours ago) - commit eae2a37
  • DOC: update list of changes [skip ci] (7 hours ago) - commit 958065f
  • Merge pull request #56 from connectomicslab/55_singularity_v3.0.0-RC2-dev (8 hours ago) - commit f2d772a
  • MAINT: correct variable name to be PEP8 compliant (17 hours ago) - commit 4e518c1
  • FIX: rename variables correctly in cmtklib/parcellation.py and correct indent (18 hours ago) - commit 853b963
  • DOC: add docstrings and reviewed indents in run.py [skip ci] (23 hours ago) - commit a48a986
  • MAINT: review name and unused variables in cmtklib/parcellation.py (24 hours ago) - commit 22e96c2
  • FIX: config files in BIDS App GUI [skip ci] (25 hours ago) - commit e9e4449
  • FIX: mapping of config files in docker run command generated by GUI [skip ci] (25 hours ago) - commit df8728a
  • MAINT: remove unnecessary parenthesis [skip ci] (26 hours ago) - commit 71f0122
  • MAINT: code cleaning (27 hours ago) - commit 1b75da6
  • MAINT: simplify expression (27 hours ago) - commit 4663f13
  • Revert "MAINT: simplify expression" (27 hours ago) - commit ac9aed2
  • MAINT: simplify expression (27 hours ago) - commit 1ce54bd
  • FIX: correct Dipy PeakAndMetrics.shm_coeffs (27 hours ago) - commit 4f29c2d
  • DOC: correct docstring issues (27 hours ago) - commit 80b4e64
  • PEP: correct all PEP8 code style errors reported by pycharm (28 hours ago) - commit 43c18ba
  • ENH: Generate docker run command in GUI with new BIDS App options flags to control RDG and multithreading [skip ci] (30 hours ago) - commit ea7559e
  • FIX: map appropriately the configuration files in the docker run command generated by the GUI [skip ci] (31 hours ago) - commit 53c5dc7
  • ENH: added new traits in the BIDS App GUI to control RDG and multi-threading and reviewed layout [skip ci] (31 hours ago) - commit 0784728
  • Merge branch 'v3.0.0-RC2-dev' into 55_singularity_v3.0.0-RC2-dev (33 hours ago) - commit b4877b9
  • REF: review list, name, and default value of parameters for RDG and multi-threading in parser.py and run.py (33 hours ago) - commit 4538ac3
  • Merge pull request #60 from connectomicslab/reproducibility_control_v3.0.0-RC2-dev (34 hours ago) - commit d066415
  • TEST: fix name of output files (34 hours ago) - commit 3f2c618
  • CI: enable and update difference check of list of outputs for singularity tests (2 days ago) - commit c87ca63
  • TEST: updated list of outputs for singularity test (2 days ago) - commit 0e90343
  • TYPO: corrected to args.set_mkl_num_threads in run.py (2 days ago) - commit d77b4e7
  • ENH: add options to BIDS App to fix multiple envvars related to random generator seed and number of threads (2 days ago) - commit 247ed73
  • MAINT: review message when report is sent to analytics [skip ci] (2 days ago) - commit 89a75c7
  • FIX: set self.number_of_threads_max and added comments for dmri/fmri data check [skip ci] (2 days ago) - commit 574e0ae
  • DOCKER: remove build-essential after building mrtrix [skip ci] (2 days ago) - commit 0f934f6
  • CI: review order of jobs to give priority to test_singularity [skip ci] (2 days ago) - commit 3a2febc
  • ENH: display configuration of diffusion and or fmri pipeline in BIDS App Window if inputs are available [skip ci] (2 days ago) - commit 7f9d988
  • DOCKER: Remove packages for qt4 and opengl libraries as mrtrix is build with -nogui [skip ci] (2 days ago) - commit 4af790b
  • DOCKER: edit cleaning of installation step of matlab for freesurfer [skip ci] (2 days ago) - commit 422de2e
  • DOC: update comment for FSL 5 python 3 patch [skip ci] (2 days ago) - commit a49611f
  • CI: review job order/dependence for singularity build and tests (2 days ago) - commit 13f9cf3
  • DOCKER: add patch from ndmg for FSL 5.0.9 and python (2 days ago) - commit c52e4d9
  • REVERT: remove v as prefix to extracted version in build_bidsapp.sh [skip ci] (2 days ago) - commit 920d2d0
  • DOCKER: remove comment that raised an empty continuation line [skip ci] (2 days ago) - commit 57212d3
  • DOCKER: fix empty continuation line (2 days ago) - commit 625de0a
  • TYPO: add v as prefix to extracted version in build_bidsapp.sh (2 days ago) - commit 53ffc89
  • DOCKER: review cleaning of docker image and install fsl 5.0.9 much more light (2 days ago) - commit 586d643
  • DOCKER: correct paths (3 days ago) - commit cb9408b
  • DOCKER: refactoring to use only one docker file with multi-stage (3 days ago) - commit 676a6ea
  • DOCKER: removed resources from .dockerignore (3 days ago) - commit b474efb
  • CONDA: move obspy (3 days ago) - commit f68ae9c
  • DOCKER: remove bin/freeview (3 days ago) - commit ff515e1
  • DOCKER: removed lib/vtk bin/qt.conf from exclude in freesurfer (3 days ago) - commit d2708a2
  • DOCKER: exclude freeview related files when extracting freesurfer (3 days ago) - commit 6f4771a
  • DOCKER: review conda bin path (3 days ago) - commit 5c29c26
  • DOCKER: add -y to apt-get remove curl (3 days ago) - commit daf20d7
  • DOCKER: add -y to apt-get remove curl (3 days ago) - commit 3aef9b2
  • CI: revert back to use docker registry for singularity build (3 days ago) - commit 5044762
  • DOCKER: clean and try to reduce layer size (3 days ago) - commit 3caeb46
  • DOCKER: add folders to be ignored in .dockerignore (3 days ago) - commit 4b9cb3c
  • CI: review singularity build with docker-deamon and show storage information (2) (3 days ago) - commit b0ba184
  • CI: review singularity build with docker-deamon and show storage information (3 days ago) - commit d154709
  • CI: add SINGULARITY_DISABLE_CACHE=true (6 days ago) - commit 76a9dce
  • CI: add --debug -v to singularity build (6 days ago) - commit 66e4972
  • CI: try to set tmp dir environment variables directly at singularity build (6 days ago) - commit 4b934d9
  • CI: try to set TMPDIR for singularity build (6 days ago) - commit 3f65016
  • FIX: docker run command generated by GUI [skip ci] (6 days ago) - commit 54e7ba3
  • FIX: updated label for sift in configurator GUI [skip ci] (6 days ago) - commit 697a97e
  • FIX: size of image icon for quality check button in main GUI [skip ci] (6 days ago) - commit c5ef30a
  • FIX: corrected sift2 -> sift [skip ci] (6 days ago) - commit 27a61ef
  • FIX: do not resize image icons for buttons of main GUI [skip ci] (6 days ago) - commit 5aba00e
  • CI: remove /tmp/cache/docker.tar.gz in job after loading (6 days ago) - commit e6118fa
  • CI: try to set different tmp cache dir for singularity build for resolving no space left on device error (6 days ago) - commit 0bae5a7
  • Merge branch 'v3.0.0-RC2-dev' into 55_singularity_v3.0.0-RC2-dev (7 days ago) - commit aaa9d6d
  • Merge pull request #52 from connectomicslab/48_sift2_v3.0.0-RC2 (7 days ago) - commit 8e96279
  • CI: show docker images to see if possible to remove one to reduce size on disk (7 days ago) - commit ab1404d
  • DOC: update usage.rst [skip ci] (7 days ago) - commit 6da7dd9
  • DOC: update changes.rst [skip ci] (7 days ago) - commit b8a819c
  • DOC: update changes.rst [skip ci] (7 days ago) - commit 4343af7
  • DOC: add changes for version 3.0.0-RC2 [skip ci] (7 days ago) - commit 261a99a
  • DOC: add warning regarding the little tracker [skip ci] (7 days ago) - commit 5b9c9d8
  • FIX: correct indent in .circleci/config.yml (7 days ago) - commit 7239aa4
  • FIX: correct typo in .circleci/config.yml (7 days ago) - commit 68bd9f3
  • ENH: add jobs to build, test and deploy the singularity image to sylabs.io (#55) (7 days ago) - commit 46d6ff5
  • FIX: corrected code (7 days ago) - commit 37b46c5
  • TEST: updated list of outputs and re-enable diff check for tests 01 and 02 (7 days ago) - commit 7c18c83
  • MAINT: code layout (8 days ago) - commit 94236d3
  • ENH: use SIFT instead of SIFT2 to filter tractogram (8 days ago) - commit 9688410
  • FIX: add act_file input to FilterTractogram (8 days ago) - commit 2609789
  • DOC: add new sift2 config to docstring (8 days ago) - commit a30fe9c
  • REV: review rescaled images of buttons for GUI windows (8 days ago) - commit 32f18b0
  • MAINT: code cleaning and code style in cmpbidsa...
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Assets 2