Version 3.0.0-beta-RC2

Date: June 02, 2020

This version integrates Pull Request #33 which includes in particular:


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

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 @
  • 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