Release 0.10.1

Fixed

• [IOTools] Fix merge-tsv tool and its caps option (PR #1535)
• [Dependencies] Update dependencies and perform associated fixes (PR #1531)

Release 0.10.0

Fixed

• [IOTools] Fix broken import of bids.dataset module (PR #1484)
• [IOTools] Center-Nifti now runs by default on T1 as it was expected (PR #1418)
• [DWI] Fix broken import of bids.dataset module (PR #1523)
• [Converters] GENFI : Fix validation of optional path to clinical data (PR #1513)
• [Pipelines] Fix SPM standalone version check (PR #1488)

Enhanced

• [Pipelines] Search for SPM standalone version is not hardcoded to SPM12 anymore (PR #1490)
• Improve architecture for BIDS and CAPS datasets logic (PR #1453)

Added

• [IOTools] When using Center-Nifti it is now possible to choose the centering threshold (PR #1433)
• [DOC] Warning about SPM standalone version (PR #1496)
• [T1Volume] Skip processed visits (PR #1403)
• [AIBL-to-BIDS] Now has a json constructor based on dicoms to retrieve information required to fit BIDS specifications (PR #1500)

Removed

• [Pipelines] Remove interactivity when centering images is required by the pipeline (PET-Volume, T1-Volume, PET-Surface, T1-Freesurfer) (PR #1419)

Release 0.9.4

Fixed

• [PET] Fix query pattern when a tracer is specified but not the reconstruction method (see PR #1470)
• [Converters] Fix type mismatch in clinica.iotools.bids_utils (see PR #1376)

Release 0.9.3

Fixed

• [PETLinear] Fix the SUVR normalization step (see PR #1348)

Release 0.9.2

Fixed

• [Converters] Fix KeyError "APGEN" in adni-to-bids (see PR #1342)
• [Converters] Fix function load_clinical_csv to avoid hidden files (see PR #1343)
• [Converters] Fix logging in oasis-to-bids and aibl-to-bids (see PR #1340)
• [Converters] Fix method BIDSSubjectID.to_study_id() (see PR #1335)
• [T1Linear] Fix missing import in utility function (see PR #1329)
• [Converters] Fix oasis-to-bids to work with new clinical data (see PR #1321)
• [Converters] Fix function define_participants in ixi-to-bids, which is now deterministic (see PR #1318)
• [Converters] Fix Oasis1 BIDSSubjectID method (see PR #1312)

Release 0.9.1

Fixed

• Fix broken install of release 0.9.0 (see PR #1304)

Release 0.9.0

Clinica 0.9.0

Added

• [ixi-to-bids] There is a new converter to convert IXI to BIDS (see PR #1239)
• [iotools] There is a new tool clinica iotools describe to nicely display metadata in dataset_description.json files in the console (see PR #1287)
• [t1-linear] It is now possible to use t1-linear with ANTsPy (see PR #1244)
• [ADNI2BIDS] The converter now support FMAP (see PR #1119)
• [Doc] Some pages have been refactored to improve readability and make information easier to find (see PR #1284, #1288, and #1295)
• [Doc] The online documentation now has a glossary page (see PR #1110)

Breaking changes

• BIDS and CAPS datasets must have a dataset_description.json file at the root (see PR #1158)

Enhanced

• [Converters] Converters now implement the same API which make them easier to use from Python (see PR #1140)

Fixed

• [Converters] A few issues with logging have been fixed (see PR #1181)
• [t1-linear] Fix the crop_nifti function which was doing unnecessary resampling (see PR #1215)

Release 0.8.4

Fixed

• [Pipelines] Fix 'SPM not in matlab path' error when using SPM12 with Matlab (see PR #1261)

Release 0.8.3

Fixed

• [IOTools] Fix merge-tsv when providing a T1Freesurfer CAPS directory (see PR #1240).

Release 0.8.2

Fixed

• [ADNI2BIDS] Fix wrong preprocessing sequence in FDG PET Uniform (see PR #1159)
• [NIFD2BIDS] Fix check on type in pandas dataframe (see PR #1230)
• [DWI] DWIPreprocessingUsingT1 pipeline skips problematic images instead of crashing (see PR #1169)
• Fix compatibility issues with matplotlib 3.9 (see PR #1185)