Releases: aramis-lab/clinica
Releases · aramis-lab/clinica
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 aT1Freesurfer
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
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
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
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