Changes

Version 3.0.0-RC2

Date: December 24, 2020

This version corresponds to the second release candidate of Connectome Mapper 3. In particular, it integrates Pull Request #45 which includes:

New feature

• Add SIFT2 tractogram filtering (requested in #48, PR #52).

• Add a tracker to support us seeking for new funding. User is still free to opt-out and disable it with the new option flag --notrack.

• Add options suggested by Theaud G et al. (2020) to better control factors having impacts on reproducibility. It includes:

  • Set the number of ITK threads used by ANTs for registration (option flag --ants_number_of_threads).

  • Set the seed of the random number generator used by ANTs for registration (option flag --ants_random_seed).

  • Set the seed of the random number generator used by MRtrix for tractography seeding and track propagation (option flag --mrtrix_random_seed).

• Full support of Singularity (see Software development life cycle).

Code refactoring

• A number of classes describing interfaces to fsl and mrtrix3 have been moved from cmtklib/interfaces/util.py to cmtklib/interfaces/fsl.py and cmtklib/interfaces/mrtrix3.py.

• Capitalize the first letter of a number of class names.

• Lowercase a number of variable names in cmtklib/parcellation.py.

Graphical User Interface

• Improve display of qpushbuttons with images in the GUI (PR #52).

• Make the window to control BIDS App execution scrollable.

• Allow to specify a custom output directory.

• Tune new options in the window to control BIDS App multi-threading (OpenMP and ANTs) and random number generators (ANTs and MRtrix).

Documentation

• Full code documentation with numpydoc-style docstrings.

• API documentation page at readthedocs.

Bug fixes

• Fix the error reported in #17 if it is still occuring.

• Review statements for creating contents of BIDS App entrypoint scripts to fix issue with Singularity converted images reported in #47.

• Install dc package inside the BIDS App to fix the issue with FSL BET reported in #50.

• Install libopenblas package inside the BIDS App to fix the issue with FSL EDDY_OPENMP reported in #49.

Software development life cycle

• Add a new job test_docker_fmri that test the fMRI pipeline.

• Add build_singularity, test_singularity_parcellation, deploy_singularity_latest, and deploy_singularity_release jobs to build, test and deploy the Singularity image in CircleCI (PR #56).

Please check the main pull request 45 page for more details.

Version 3.0.0-RC1

Date: August 03, 2020

This version corresponds to the first release candidate of Connectome Mapper 3. In particular, it integrates Pull Request #40 where the last major changes prior to its official release have been made, which includes in particular:

Migration to Python 3

• Fixes automatically with 2to3 and manually a number of Python 2 statements invalid in python 3 including the print() function

• Correct automatically PEP8 code style issues with autopep8

• Correct manually a number of code stly issues reported by Codacy (bandits/pylints/flake8)

• Major dependency upgrades including:

  • dipy 0.15 -> 1.0 and related code changes in cmtklib/interfaces/dipy (Check here for more details about Dipy 1.0 changes)

  Warning

  Interface for tractography based on Dipy DTI model and EuDX tractography, which has been drastically changed in Dipy 1.0, has not been updated yet, It will be part of the next release candidate.

  • nipype 1.1.8 -> 1.5.0

  • pybids 0.9.5 -> 0.10.2

  • pydicom 1.4.2 -> 2.0.0

  • networkX 2.2 -> 2.4

  • statsmodels 0.9.0 -> 0.11.1

  • obspy 1.1.1 -> 1.2.1

  • traits 5.1 -> 6.0.0

  • traitsui 6.0.0 -> 6.1.3

  • numpy 1.15.4 -> 1.18.5

  • matplotlib 1.1.8 -> 1.5.0

  • fsleyes 0.27.3 -> 0.33.0

  • mne 0.17.1 -> 0.20.7

  • sphinx 1.8.5 -> 3.1.1

  • sphinx_rtd_theme 0.4.3 -> 0.5.0

  • recommonmark 0.5.0 -> 0.6.0

New feature

• Option to run Freesurfer recon-all in parallel and to specify the number of threads used by not only Freesurfer but also all softwares relying on OpenMP for multi-threading. This can be achieved by running the BIDS App with the new option flag --number_of_threads.

Changes in BIDS derivatives

• Renamed connectivity graph files to better conform to the BIDS extension proposal on connectivity data schema. They are now saved by default in a TSV file as a list of edges.

Code refactoring

• Functions to save and load pipeline configuration files have been moved to cmtklib/config.py

Bug fixes

• Major changes in how inspection of stage/pipeline outputs with the graphical user interface (cmpbidsappmanager) which was not working anymore after migration to Python3

• Fixes to compute the structural connectivity matrices following migration to python 3

• Fixes to computes ROI volumetry for Lausanne2008 and NativeFreesurfer parcellation schemes

• Add missing renaming of the ROI volumetry file for the NativeFreesurfer parcellation scheme following BIDS

• Create the mask used for computing peaks from the Dipy CSD model when performing Particle Filtering Tractography (development still on-going)

• Add missing renaming of Dipy tensor-related maps (AD, RD, MD) following BIDS

• Remove all references to use Custom segmentation / parcellation / diffusion FOD image / tractogram, inherited from CMP2 but not anymore functional following the adoption of BIDS standard inside CMP3.

Software development life cycle

• Use Codacy to support code reviews and monitor code quality over time.

• Use coveragepy in CircleCI during regression tests of the BIDS app and create code coverage reports published on our Codacy project page.

• Add new regression tests in CircleCI to improve code coverage:

  • Test 01: Lausanne2018 (full) parcellation + Dipy SHORE + Mrtrix3 SD_STREAM tractography

  • Test 02: Lausanne2018 (full) parcellation + Dipy SHORE + Mrtrix3 ACT iFOV2 tractography

  • Test 03: Lausanne2018 (full) parcellation + Dipy SHORE + Dipy deterministic tractography

  • Test 04: Lausanne2018 (full) parcellation + Dipy SHORE + Dipy Particle Filtering tractography

  • Test 05: Native Freesurfer (Desikan-Killiany) parcellation

  • Test 06: Lausanne2008 parcellation (as implemented in CMP2)

• Moved pipeline configurations for regression tests in CircleCI from config/ to .circle/tests/configuration_files

• Moved lists of expected regression test outputs in CircleCI from .circle/ to .circle/tests/expected_outputs

Please check the pull request 40 page for more details.

Version 3.0.0-beta-RC2

Date: June 02, 2020

This version integrates Pull Request #33 which corresponds to the last beta release that still relies on Python 2.7. It includes in particular:

Upgrade

• Uses fsleyes instead of fslview (now deprecated), which now included in the conda environment of the GUI (py27cmp-gui).

New feature

• Computes of ROI volumetry stored in <output_dir>/sub-<label>(/ses<label>)/anat folder, recognized by their _stats.tsv file name suffix.

Improved replicability

• Sets the MATRIX_RNG_SEED environment variable (used by MRtrix) and seed for the numpy random number generator (numpy.random.seed())

Bug fixes

• Fixes the output inspector window of the cmpbidsappmanager (GUI) that fails to find existing outputs, after adoption of /bids_dir and /output_dir in the bidsapp docker image.

• Fixes the way to get the list of networkx edge attributes in inspect_outputs() of ConnectomeStage for the output inspector window of the cmpbidsappmanager (GUI)

• Added missing package dependencies (fury and vtk) that fixes dipy_CSD execution error when trying to import module actor from dipy.viz to save the results in a png

• Fixes a number of unresolved references identified by pycharm code inspection tool

Code refactoring

• Interfaces for fMRI processing were moved to cmtklib/functionalMRI.py.

• Interface for fMRI connectome creation (rsfmri_conmat) moved to cmtklib/connectome.py

Please check the pull request 33 page for change details.

Version 3.0.0-beta-RC1

Date: March 26, 2020

This version integrates Pull Request #28 which includes in summary:

• A major revision of continuous integration testing and deployment with CircleCI which closes Issue 14 integrates an in-house dataset published and available on Zenodo @ https://doi.org/10.5281/zenodo.3708962.

• Multiple bug fixes and enhancements incl. close Issue 30 , update mrtrix3 to RC3 version, bids-app run command generated by the GUI, location of the configuration and log files to be more BIDS compliant.

• Change in tagging beta version which otherwise might not be meaningfull in accordance with the release date (especially when the expected date is delayed due to unexpected errors that might take longer to be fixed than expected).

Please check the pull request 28 page for a full list of changes.

Version 3.0.0-beta-20200227

Date: February 27, 2020

This version addresses multiple issues to make successful conversion and run of the CMP3 BIDS App on HPC (Clusters) using Singularity.

• Revised the build of the master and BIDS App images:

  • Install locales and set $LC_ALL and $LANG to make freesurfer hippocampal subfields and brainstem segmentation (matlab-based) modules working when run in the converted SIngularity image

  • BIDS input and output directories inside the BIDS App container are no longer the /tmp and /tmp/derivatives folders but /bids_dir and /output_dir. .. warning:: this might affect the use of Datalad container (To be confirmed.)

  • Fix the branch of mrtrix3 to check out

  • Updated metadata

• Fix the configuration of CircleCI to not use Docker layer cache feature anymore as this feature is not included anymore in the free plan for open source projects.

• Improved documentation where the latest version should be dynamically generated everywhere it should appear.

Version 3.0.0-beta-20200206

Date: February 06, 2020

• Implementation of an in-house Nipype interface to AFNI 3DBandPass which can handle to check output as ..++orig.BRIK or as ..tlrc.BRIK (The later can occur with HCP preprocessed fmri data)

Version 3.0.0-beta-20200124

Date: January 24, 2020

• Updated multi-scale parcellation with a new symmetric version:

  1. The right hemisphere labels were projected in the left hemisphere to create a symmetric version of the multiscale cortical parcellation proposed by Cammoun2012.

  2. For scale 1, the boundaries of the projected regions over the left hemisphere were matched to the boundaries of the original parcellation for the left hemisphere.

  3. This transformation was applied for the rest of the scales.

• Updated documentation with list of changes