Changes¶
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() functionCorrect 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 incmtklib/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 offslview
(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()
ofConnectomeStage
for the output inspector window of the cmpbidsappmanager (GUI) - Added missing package dependencies (
fury
andvtk
) 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 tocmtklib/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
- Install locales and set
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:
- The right hemisphere labels were projected in the left hemisphere to create a symmetric version of the multiscale cortical parcellation proposed by Cammoun2012.
- 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.
- This transformation was applied for the rest of the scales.
Updated documentation with list of changes