Version 0.2.0

Changes

Clinica Core:

• [Update] Clinica is now using Python 3.6.0 & Nipype 1.1.2.
• [New] A CI framework is set up for Clinica.
• [Improvement] General improvements include better error handling/message when executing Clinica.
• [New] Clinica checks if there is sufficient space before running a pipeline.
• [New] Clinica ensures that multithreading is used before running a pipeline, and warns the user otherwise.
• [Fix] Relative path in command line now works properly.
• [New] The Clinica project is now PEP8 compliant.

Pipelines:

• [New] machinelearning-prepare-spatial-svm pipeline: Prepare input data for spatially regularized SVM [Cuingnet et al, 2013]. More info on the Wiki: http://www.clinica.run/doc/Pipelines/MachineLearning_PrepareSVM/
• [New] fmri-preprocessing pipeline: fMRI pre-processing with slice timing and motion correction, brain extraction and spatial normalization. More info on the Wiki: http://www.clinica.run/doc/Pipelines/fMRI_Preprocessing/
• [Change] The dwi-processing-noddi (and its prerequisites dwi-preprocessing-multi-shell) is removed from the Clinica software as we will not actively maintain it. It is now on a separate repository: https://github.com/aramis-lab/clinica_pipeline_noddi
• [Fix] t1-freesurfer now handles FreeSurfer 6.0.0.
• [Change] New pipeline names :
  • t1-freesurfer-cross-sectional becomes t1-freesurfer;
  • t1-spm-* pipelines become t1-volume-*. In particular, t1-spm-full-prep is now t1-volume and t1-volume-existing-dartel is now t1-volume-existing-template;
  • dwi-preprocessing-using-phasediff-fieldmap is now dwi-preprocessing-using-fieldmap;
  • dwi-processing-dti pipeline becomes dwi-dti;
  • pet-preprocessing-volume pipeline becomes pet-volume.

Converters:

[New] The ADNI-2-BIDS converter now includes the diffusion MRI and FLAIR sequences.

IOTools:

[Fix] Fix merge-tsv command line when no path was given to the TSV file.
[New] The merge-tsv can now parse TSV files from CAPS. Currently, it only supports the t1-volume and pet-volume pipelines.