Clinica v.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 v0.5.3 Bugfixes

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 v0.5.2 Dwi-preprocessing upgrade / bugfixes

Clinica 0.5.2

Changed

[DWI-preprocessing] Rewrite of DWI-preprocessing pipelines using FSL's eddy tool

Removed

[DeepLearningPrepareData] Migrated deeplearning-prepare-data to ClinicaDL

Fixed

[Oasis3/NIFD] Fix code for backward compatibility with pandas 1.1.x
[T1-Freesurfer/DWI] Remove Typing for compatibility with Nipype
[T1Volume] Add command line option to prevent interactive prompts

0.5.1 - Introducing Oasis3 Converter

Added

• [Oassis3-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
• [iotools]Fix bug on empty dataframe
• [CI] Fix bash instruction to init conda-
• [doc] Correct DWI-Connectome description paragraph

0.5.0 - Code Optimization - ROI extraction in DLPrepapreData

Clinica 0.5 -

Added

• [Docs] 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 converter] Optimization of adni2bids clincal data extraction
• [ADNI converter] Replace xlsx by tsv files for clinical data specification
• [Converters] Remove dcm2nii fallback
• [AIBL converter] Remove freesurfer fallback and dependency

Fixed

• [Core] fix bug in write_scan_tsv
• [Docs] Add documentation for check-missing-processing
• [Docs] Fix several small typos
• [Docs] 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
• [Iotools] fix indices in merge-tsv
• [ML] Fix unresolved reference in SVM pipeline
• [ML] Fix typo in parameters for SVC pipeline

Clinica v0.5.0rc1 improved logging, CLI, And adni-to-bids. Experimental ROI extraction in DLPrepapre data

Clinica 0.5rc1 -

Added

• [Docs] 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 converter] Optimization of adni2bids clincal data extraction

• [Adni converter] Replace xlsx by tsv files for clinical data specification

Fixed

• [Core] fix bug in write_scan_tsv
• [Docs] Add documentation for check-missing-processing
• [Docs] Fix several small typos
• [Docs] Instructions for installing SPM dependency on MacOs Big Sur
• [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 - Deeplearning-prepare-data (for pet-linear output), converters updates and some minor fixes

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.
• [ADNI-to-bids]: Update image selection to always consider non-processed (original) images
• [merge-tsv]: Fetch sub-cortical volumes generated by t1-freesurfer pipelines and JSON
  files (if exists).

Fixed

• [pet-surface]: Verify SPM12 installation when running pipeline
• [docs]: Update instruction to install some third party software

Clinica 0.4.0 - PET-Linear, PET-Surface-Longitudinal, Harmonization & Refactor

Changes

Clinica core:

• [Enh] Code source was completely reformatted using the Black code style.
• [Enh] Documentation for the project is now versioned (versions from 0.3.8 are publicly available).
• [Enh] Functions used for multiple pipelines are now mutualized (e.g container_from_filename function).
• [Enh] f-strings are used massively.

Pipelines:

• [New] pet-linear pipeline: spatial normalization to the MNI space and intensity normalization of PET images. More info in the wiki: https://aramislab.paris.inria.fr/clinica/docs/public/latest/Pipelines/PET_Linear/
• [New] pet-surface-longitudinal pipeline: Surface-based longitudinal processing of PET images [Marcoux et al., 2018]. More info in the wiki: https://aramislab.paris.inria.fr/clinica/docs/public/latest/Pipelines/PET_Surface_Longitudinal/
• [New] Harmonize output message display when running a pipeline.
• [New] Automatically ignore an image to process if it is found in the CAPS folder.
• [Fix] Fix a minor bug when the pet-volume pipeline performs PVC.

Converters:

• [Enh] Conversion information is added once the converter is run to facilitate traceability.
• [Enh] Add new keywords available in ADNI3 to the adni-2-bids converter.

IOtools:

• [New] check-missing-processing tool allows creating a TSV file containing information about the pipelines executed into a specific CAPS folder.

Clinica 0.3.8

Added

• Add option to run deeplearning-prepare-data in output of t1-extension pipeline and
  also 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:

• [New] t1-freesurfer-longitudinal pipeline: FreeSurfer-based longitudinal processing of T1-weighted MR images [Reuter et al., 2012]. More info in the wiki: http://www.clinica.run/doc/Pipelines/T1_FreeSurfer_Longitudinal/
• [Change] The fmri-preprocessing pipeline is removed from the Clinica software as we will not actively maintain it. It is now in a separate repository: https://github.com/aramis-lab/clinica_pipeline_fmri_preprocessing

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