Clinica 0.3.3

Changes

Clinica Core:

• [New] Use PEP8 Speaks tool for PEP8 checks.
• [Improvement] Improve Jinja2 template.

Pipelines:

• [New] t1-linear - Affine registration of T1w images to the MNI standard space. More info on the Wiki: http://www.clinica.run/doc/Pipelines/T1_Linear .
• [New] statistics-volume and (experimental) statistics-volume-correction - Volume-based mass-univariate analysis with SPM. More info on the Wiki: http://www.clinica.run/doc/Pipelines/Stats_Volume .
• [Fix] Error for pet-surface pipeline with unzipped files (Issue #68).
• [Improvement] Improve error message in pet-surface when metadata are missing in JSON file (Issue #69).
• [Fix] Prevent Clinica from running PET pipelines on 4D volumes (Issue #70).
• [Fix] Display clear error message when trying to create a DARTEL template with one image (Issue #74).
• [Fix] Fix bug where CAPS outputs for t1-freesurfer pipeline were not saved (Google Groups).

Converters:

• [Fix] Fix wrong path for BIDS FLAIR MR image, missing JSON files for DWI, error when generating paths for AV45 and Florbetaben PET images for adni-2-bids(Issue #50).
• [New] Add new fields to clinical data in adni-2-bids e.g. Clinical Dementia Rating Scale (CDR), Montreal Cognitive Assessment (MOCA). The full list is located in the file clinica/iotools/data/clinical_specifications_adni.xlsx.
• [Improvement] General improvements for adni-2-bids are detailed in PR #55 and merged in PR #64.