Version 0.3.0

Changes

Clinica Core:

• [Improvement] General improvements include better error handling/message when executing Clinica (missing dependency, BIDS/CAPS handling, typos, warning messages).
• [Fix] After fixing "Assuming non interactive session since isatty found missing" for Clinica 0.2.2, Clinica became too verbose when running a pipeline (Issue #7). An alternative bugfix was used.
• [New] Add timeout when asking if pipeline starts even though disks are full
• [New] Add timeout when asking user for n_procs
• [New] Detect if extra flags are given and if -v is used after clinica {run|iotools|convert}
• [New] Add warning message if PYTHONPATH is not empty (should avoid this situation)

Pipelines:

• [New] dwi-connectome pipeline: Construction of structural connectome with computation of fiber orientation distributions, tractogram and connectome. More info on the Wiki: http://www.clinica.run/doc/Pipelines/DWI_Connectome
• [Change] t1-freesurfer pipeline was rewritten. It includes a complete refactoring and:
  • The pipeline is now executed in the working directory and outputs without errors from FreeSurfer or Nipype are now copied from the working directory to the CAPS folder;
  • the symbolic links (e.g. fsaverage) are not present in the CAPS folder anymore;
  • If Clinica fails on some images, it detects & displays the subjects who failed.
• [Change] The TSV files generated by the t1-freesurfer* pipelines are now ordered in two columns (name, value)- [Fix] Fix parallelization in t1-volume-tissue-segmentation and t1-volume-existing-template pipelines: if SPM failed on an image, Clinica did not manage to save successful results of other images in CAPS directory
• [Fix] Remove atlas statistics generation in t1-volume-dartel2mni pipeline
• [Fix] Check the presence of CAT12 in volume pipelines. Otherwise, the pipeline failed when trying to generate statistics for atlases part of the CAT12 toolbox.
• [Fix] Include Matlab files from ‘pipelines’ folder when using the user installation (i.e. without pip -e .). Otherwise, pet-volume pipeline failed.
• [Fix] Sort diagnosis list to avoid mixing labels when testing for ML modules.
• [Update] Edit path to search Tissue Probability Map in SPM standalone.
• [Update] Remove several obsolete functions and workflows.

Converters:

• [Update] The adni-2-bids converter now includes ADNI3 and new modalities (fMRI, PET data)
• [New] nifd-2-bids converter: You can now convert the NIFD dataset (http://4rtni-ftldni.ini.usc.edu) into BIDS. More info on the Wiki: http://www.clinica.run/doc/DatabasesToBIDS/#nifd-to-bids
• [Fix] Fix age in sessions.tsv file for adni-2-bids (the age was the same across sessions)
• [New] Compute age from date of birth and date of exam for aibl-2-bids
• [Improvement] Deduce missing examination dates in aibl-2-bids
• [Fix] Remove duplicates in oasis-2-bids converter

IOTools:

• [Fix] Fix missing modalities bug where FLAIR and T1w could be miscounted
• [Improvement] Improve error message for iotools commands (e.g. when `-tsv is not a file, when BIDS parameter is not a folder)