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

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