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

Release 0.7.4

Clinica 0.7.4

Enhanced

• [DWI] Read total readout time and phase encoding direction from JSON files
• [IOTools] Session numbers are now represented using three digits instead of two
• [PET] Handle 4D images with dummy fourth dimension
• [Dependencies] Upgrade Poetry lock files to version 2

Added

• [Converters] New GENFI to BIDS converter
• Support for Python 3.11

Fixed

• [BUG] Fixed issue with NetworkX 3
• [BUG] Fix run statistics-volume-correction assertion error
• [DOC] Fix command in statistics volume documentation
• [IOTools] Fix create_scan_dict row extraction condition

Release v0.7.3

Clinica 0.7.3

Enhanced

• [CI] Add caching support for unit tests
• [CI] Refactor testing tools
• [Dependencies] Bump lxml from 4.9.0 to 4.9.1
• [Dependencies] Upgrade joblib to 1.2.0
• [Dependencies] build: Install nipype up to version 1.8.2
• [SurfStat] Pure python implementation
• [IOTools] Fix warnings in merge-tsv
• [Adni2BIDS] Deal with new data from ADNI3
• [DWIPreprocessingUsingT1] Optimized disk usage of Pipeline DWIPreprocessingUsingT1
• [IOTools] Allow setting a custom logging directory via environment variable
• [IOTools] Center all modalities if no modality is specified
• [Pipelines] Report uncompliant BIDS subjects

Added

• [Converters] Add support for BIDS Readme
• [IOTools] Extend the create-subjects-sessions iotool to CAPS directories
• [IOTools] Add pet-linear to checks for missing processing

Fixed

• [UKB2BIDS] Add error if data is not found or filtered
• [DWIPreprocessingUsingT1] Add missing out_file parameter to DWIBiasCorrect
• [Converters] UKB2BIDS drop directories labeled as unusable
• [Adni2BIDS] Handle empty lines in create_subs_sess_list
• [IOTools] Fix vox_to_world_space_method_1

Release v0.7.2

Clinica 0.7.2

Fixed

• [Pipelines] Fix bug introduced in previous version with the use of the gunzip interface
• [DWIConnectome] Use ConstrainedSphericalDeconvolution instead of buggy EstimateFOD

Enhanced

• [Adni2Bids] Add compatibility for edge cases introduced in Adni3

Release v0.7.1

Added

• [Doc] add ukbiobank documentation
• [DWIConnectome] Fetch meta data directly from MRtrix github repository

Changed

• [Core] Enable parallelelization when grabbing files

Fixed

• [Converters] Fix several warnings

Release v0.7.0

New

• [flair-linear] new pipeline to affinely align FLAIR images to the MNI space
• [Ukbiobank] new converter to modify T1W/T2/DWI/SWI/tfmri/rsfMRI UKBiobank data into BIDS standard