Version 0.3.1

Changes

Clinica Core:

• [Fix] Remove the double equal from conda environment file, to be compatible with conda > 4.7
• [New] Add clinica_file_reader / clinica_group_reader functions to read input files for Clinica
• [New] Add ux.py to centralize output message for each pipeline (currently used in t1-freesurfer pipeline)
• [Enh] Improve verifications in check_bids_folder / check_caps_folder
• [Enh] Improve how Clinica handles SPM/SPM-Standalone on Mac/Linux and how Clinica extracts TPM file.
• [Enh] Replace duplicated code by calls of check_spm, check_cat12 and check_environment function
• [Enh] Remove obsolete functions

Pipelines:

• [Fix] Check volume locations in t1-freesurfer and t1-volume pipelines
  • For t1-freesurfer, this check is useful if the user plans to use pet-surface afterwards.
  • For t1-volume, this check is important since SPM Segment() expects centers of T1w images to be closed to 0.
• [Fix] Check relative volume locations in pet-surface and pet-volume pipelines. In these pipelines, SPM Coregister() method is used to register T1w and PET images. However, if the centers of these images are far from each other, this registration may fail
• [Enh] Rewrite build_input_node method for all pipelines
• [Enh] Harmonize exception handling when missing or duplicated BIDS/CAPS files are present for all pipelines
• [Enh] Change how to find NaN values in images
• [Fix] t1-freesurfer: Fix the sending of argument for -raa/--recon_all_args flag

IOTools:

• [New] Add center-nifti IOTool to center NIfTI files of a BIDS directory. This tool is mainly used when SPM is not able to segment some T1w images because the centers of these volumes are not aligned with the origin of the world coordinate system. By default, only problematic images are converted. The rest of the images are also copied to the new BIDS directory, but left untouched.