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

Clinica v.0.6.0

Changed

• [PET*] Use trcinstead of acq for BIDS compliance
• [Converters] Remove supperfluous use of acq entity in filenames for BIDS compliance

Added

• [adni-to-bids] allow extraction of metadata from xml
• [CI] Initiate use of unit tests

Fixed

• [adni-to-bids] fix edge case for supporting nan session-ids

Version 0.5.6

Fixed

• [DWIPreprocessUsingT1] Updated call to antsApplyTransform
• [Utils] Replace deprecated call to pandas append by concat

Changed

• Upgrade minimum Python versino to 3.8 and upgrade dependencies
• Set BIDS version to 1.7.0 by default (overwritten for some converters)

Clinica v.0.5.5

Hotfix

• Fix pet-linear infinite loop problem