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)

Release 0.8.1

Fixed

• [ADNI2BIDS] Fix DXSUM_PDXCONV_ADNIALL unknown clinical file for adni-to-bids converter (see PR #1144)
• [DWI] Fix DWI preprocessing using T1 rename to caps node (see PR #1146)

Release 0.8.0

Added

• Python 3.12 is officially supported (see PR #1065)

Breaking changes

• [DWI] Improve BIDS compliance for DWI preprocessing pipelines (see PR #1050)
• Python 3.8 is not supported anymore (see PR #1065)

Enhanced

• [ADNI2BIDS] The converter now takes fmri multiband into account (see PR #1041)
• [DWI] Set the random seed in pipelines using ANTs (requires having ANTs >= 2.5) (see PR #1071)
• [Pipelines] Using SPM standalone only requires to set $SPMSTANDALONE_HOME and $MCR_HOME (see PR #1105)
• [DOC] The Third-party documentation page has been improved (see PR #1099)
• [DOC] The documentation page for StatisticsSurface has been updated (see PR #1100)

Fixed

• [ADNI2BIDS] Ignore real and imaginary scans outputted by dcm2niix (see PR #1029)
• [ADNI2BIDS] Ignore ADC DWI images outputted by dcm2niix (see PR #1061)

Release 0.7.7

Enhanced

• [ADNI2BIDS] Enable converter to read CSV files with new naming convention from ADNI (see PR #1016)
• [Converters] Expose n_procs option to converters using multiprocessing (see PR #1009)
• [GENFI2BIDS] Enable converter to extract more clinical data (see PR #1005)

Fixed

• [IOTools] Fix regression in merge-tsv command (see PR #1013 and #1019)
• [GENFI2BIDS] Fix issue with link and readme data not found by the converter (see PR #1015)
• [PETLinear] Fix the CLI of PETLinear due to previously added option (see PR #1004)
• [T1Linear] Fix bad session labels in output file names (see PR #1000)
• [StatisticsSurface] Some fixes to the pipeline (see PR #840)

Release 0.7.6

Enhanced

• [Pipelines] The clinica file reader now supports the run entity and picks the latest run available by default (see PR #943)
• [ADNI2BIDS] The ADNI2BIDS converter now handles PET uniform data (see PR #703)
• [PETLinear] Improve the BIDS compliance of the CAPS output (see PR #935)
• [T1Linear & FLAIRLinear] Improve the BIDS compliance of the CAPS output (see PR #940)

Fixed

• [DWI] Fix regression in pipeline DWIPreprocessingUsingT1 which was not generating bvec file since release 0.7.4 (see PR #967)
• [ADNI2BIDS] Fix broken assertion in the metadata reader for derived images (see PR #957)
• [ADNI2BIDS] Fix BIDS violations in converter's output (see PR #959)

Release 0.7.5

Enhanced

• [Converters] Improvements to GENFI to BIDS converter
• [Converters] Improvements to Oasis3 to BIDS converter
• [Pipelines] Add the possibility to specify a random seed to be used with ANTs

Fixed

• [Converters] GENFI to BIDS various fixes
• [Converters] Fix ADNI to BIDS issue with unsupported visit code "uns1"
• [MachineLearning] Fix bug in CLI of pipeline machinelearning-prepare-spatial-svm