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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 0.7.2

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 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

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 clincal data extraction
  • [adni-to-bids] Replace xlsx by tsv files forclinical 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 depency 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 piplines 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