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Changelog

Main changes to this code/ project are documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Clinica 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)

Clinica 0.9.1

Fixed

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

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 #1127 and 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)

Clinica 0.8.4

Fixed

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

Clinica 0.8.3

Fixed

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

Clinica 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)

Clinica 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)

Clinica 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)

Clinica 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)

Clinica 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)

Clinica 0.7.5

Enhanced

  • [Converters] Improvements to GENFI to BIDS converter (see PR #909)
  • [Converters] Improvements to Oasis3 to BIDS converter (see PR #911)
  • [Pipelines] Add the possibility to specify a random seed to be used with ANTs (see PR #916)

Fixed

  • [Converters] GENFI to BIDS various fixes (see PRs #912, #923, #927, #930, and #934)
  • [Converters] Fix ADNI to BIDS issue with unsupported visit code "uns1" (see PRs #914 and #920)
  • [MachineLearning] Fix bug in CLI of pipeline machinelearning-prepare-spatial-svm (see PR #910)

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

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

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

Clinica 0.7.1

Added

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

Changed

  • [Core] Enable parallelization when grabbing files

Fixed

  • [Converters] Fix several warnings

Clinica 0.7.0

Added

  • [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 0.6.0

Changed

  • [PET*] Use trcinstead of acq for BIDS compliance
  • [Converters] Remove superfluous 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

Clinica 0.5.6

Fixed

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

Changed

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

Clinica 0.5.5

Fixed

  • [pet-linear] fix bug in pet-linearwhich had the pipeline not terminate

Clinica 0.5.4

Added

  • [merge-tsv] Add t1-freesurfer-longitudinal and dwi-dti results

Changed

  • [t1-freesurfer] Enable t1-freesurfer to run with missing files
  • [all converters] Normalize subprocess calls to dcm2niix

Fixed

  • [OASIS3/NIFD/HABS]] add data_description file to BIDS
  • [DWI-DTI] Remove thresholding for DECFA
  • [adni-to-bids] Tighten check on session-id values
  • [adni-to-bids] Fix bug related to multiple conversions

Clinica 0.5.3

Added

  • [t1-freesurfer] Add option to t1-freesurfer to project the results of recon-all onto another atlas
  • [CI] Use poetry for dependency management

Changed

  • [CI] Refactor non-regression tests for easier parallelization
  • [Atlas] Update checksum to make pipelines compatible with fsl 6.0.5

Fixed

  • [t1-volume*/pet*] Add command line argument yes for turning interactivity off
  • [`t1-volume-existing-template] Fix chained invocation
  • [t1-volume*/pet-volume*] Fix default value of--smooth` parameter for click compatibility
  • [dwi-connectome] Set --n_tracks's type for click compatibility
  • [dwi-preprocessing*] Change type of initrand and use_cuda to bool
  • [t1-freesurfer-longitudinal] Fix broken pipeline due to typo in code
  • [Documentation] Update OASIS3_to_bids instructions for conversion
  • [StatisticsSurface] Fix type in covariate argument
  • [StatisticsVolume] Fix bug in feature argument

Clinica 0.5.2

Changed

  • [dwi-preprocessing*] Rewrite of dwi-preprocessing* pipelines using FSL's eddy tool

Removed

  • [deeplearning-prepare-data] Migration of pipeline to ClinicaDL

Fixed

  • [oasis3-to-bids/nifd-to-bids] Change code for backward compatibility with pandas 1.1.x
  • [T1-FreeSurfer/DWI] Remove Typing for compatibility with Nipype

Clinica 0.5.1

Added

  • [oasis3-to-bids] Add converter
  • [GitHub] Add citation file

Changed

  • [adni-to-bids] Improve fetching of participants
  • [adni-to-bids] Image path finder more robust
  • [Doc] Update the OASIS3 documentation
  • [CI] Code refactoring/cleanup

Fixed

  • [Atlas] Fix ROI index for left amygdala in AAL2 atlas
  • [adni-to-bids] Prevent crash when files exists
  • [adni-to-bids] Revert behavior to encode Dementia as AD
  • [adni-to-bids] Remove entries with incoherent session names
  • [nifd-to-bids] Several bugfixes and enhancements
  • [I/O tools] Fix bug on empty dataframe
  • [CI] Fix bash instruction to init conda
  • [Doc] Correct DWI-Connectome description paragraph

Clinica 0.5.0

Added

  • [Doc] Add missing documentation on check-missing-processing iotool
  • [deeplearning-prepare-data]: Add option to run pipeline with ROI for tensor_format option to extract region of interest according to a mask.

Changed

  • [Core] Improve Logging for Clinica
  • [Core] Improve CLI through using Click
  • [Core] Nibabel replace get_data() by get_fdata() method for dataobj_images (nibabel)
  • [adni-to-bids] Optimization of adni-to-bids clinical data extraction
  • [adni-to-bids] Replace xlsx by tsv files for clinical data specification

Fixed

  • [Core] Fix bug in write_scan_tsv function
  • [Doc] Add documentation for check-missing-processing command
  • [Doc] Fix several small typos
  • [Doc] Instructions for installing SPM dependency on MacOs Big Sur
  • [CI] Fix several small issues with non-regression tests
  • [CI] Fix typo in Jenkins script
  • [CI] Automatically delete conda environments after PR is merged
  • [ML] Fix unresolved reference in SVM pipeline
  • [ML] Fix typo in parameters for SVC pipeline

Clinica 0.4.1

Added

  • [deeplearning-prepare-data]: Add option to run pipeline with pet-linear outputs

Changed

  • [oasis-to-bids]: Remove FSL library dependency for OASIS-to-bids conversion.
  • [Clinica]: Replace exception by warning when CAPs folder not recognized.
  • [aibl-to-bids]: Center output nifti files of AIBL.
  • [aibl-to-bids]: Extracts DICOM metadata in JSON files.
  • [merge-tsv]: Fetch subcortical volumes generated by t1-freesurfer pipelines and JSON files (if exists).
  • Fix minor typos in documentation.

Fixed

  • [pet-surface]: Verify SPM12 installation when running pipeline

Clinica 0.4.0

Added

  • pet-linear pipeline: spatial normalization to the MNI space and intensity normalization of PET images
  • pet-surface-longitudinal pipeline: Surface-based longitudinal processing of PET images
  • check-missing-processing tool allows creating a TSV file containing information about the pipelines executed into a specific CAPS folder
  • Conversion information is added once the converter is run to facilitate traceability.
  • Add new keywords available in ADNI3 to the adni-to-bids converter

Changed

  • Harmonize output message display when running a pipeline.
  • Automatically ignore an image to process if it is found in the CAPS folder.

Fixed

  • Fix a minor bug when the pet-volume pipeline performs PVC.
  • Code source was completely reformatted using the Black code style.
  • Documentation for the project is now versioned (versions from 0.3.8 are publicly available).
  • Functions used for multiple pipelines are now mutualized (e.g container_from_filename function).
  • f-strings are used massively.

Clinica 0.3.8

Added

  • Add option to run deeplearning-prepare-data in output of t1-extension pipeline and custom pipelines (PR #150).
  • Add Build and publish documentation with CI (PR #146).
  • Add CHANGELOG.md file

Changed

  • Harmonize PET tracers handling (ML/DL/Stats) (PR #137).
  • Behaviour of ADNI converter: some minor bugs and updated wrt ADNI3. E.g., the field age_bl was added. (PR #139, #138, #140, #142)

Fixed

  • Add DataDictionary_NIFD_.xlsx file when using NIFD2BIDS.

Clinica 0.3.7 - FreeSurfer-Longitudinal

Changes

Clinica Core:

  • [New] Remove CAT12 from dependencies
  • [New] Add checksum for volume atlases
  • [Fix] Remove duplicated lines in AICHA ROI file
  • [New] Integrate clinica.wiki repository into clinica repository: New versions of Clinica will now have their own version of documentation

Pipelines:

Converters:

  • [Enh] Improve how dependencies are checked for converters
  • [Fix] Add diagnosis conversion for ADNI3
  • [Fix] Avoid creation of sessions ses-V01 in *_sessions.tsv files

Clinica 0.3.6 - Pip

Changes

Clinica Core:

  • [Change] Pip is the main way to install Clinica. Conda packages are not available for the new versions.
  • [Update] Set the minimal version of Python to 3.7.
  • [Fix] Remove non-breaking spaces.

Pipelines:

  • [New] Display failed image(s) when running t1-linear pipeline.

Converters:

  • [Fix] The aibl-to-bids converter now handles new version of clinical data.
  • [Update] The oasis-to-bids converter now uses NiBabel instead of FreeSurfer to convert OASIS dataset.

Clinica 0.3.5 - DL-Prepare-Data

Changes

Clinica Core:

  • [CI] Improve Jenkins configuration (Automatic generation of testing reports in order to be displayed in the CI interface; Recreate Python environment if requirements.txt changes)

Pipelines:

  • [New] deeplearning-prepare-data pipeline: Prepare input data for deep learning with PyTorch. More info on the Wiki: https://aramislab.paris.inria.fr/clinica/docs/public/latest/Pipelines/DeepLearning_PrepareData/
  • [Change] t1-linear pipeline now crops image on default. If --uncropped_image is added to the command line, the image is not cropped.
  • [Change] Refactor machine learning modules. Main changes involve use of CamelCase convention for classes and parameters used dictionaries.

Clinica 0.3.4 - Bugfixes

Changes

Clinica Core:

  • [Improvement] Remove Clinica dependencies while updating and unfreezing some of them

Pipelines:

  • [Enh] Improve how template files are downloaded for t1-linear and statistics-volume pipelines

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