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 0.9.1¶
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 indataset_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 aT1Freesurfer
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
trc
instead ofacq
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
byconcat
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 inpet-linear
which had the pipeline not terminate
Clinica 0.5.4¶
Added¶
- [
merge-tsv
] Addt1-freesurfer-longitudinal
anddwi-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 onsession-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 ofrecon-all
onto another atlas - [
CI
] Usepoetry
for dependency management
Changed¶
- [
CI
] Refactor non-regression tests for easier parallelization - [
Atlas
] Update checksum to make pipelines compatible withfsl 6.0.5
Fixed¶
- [
t1-volume*/pet*
] Add command line argumentyes
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 ofinitrand
anduse_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 incovariate
argument - [
StatisticsVolume
] Fix bug infeature
argument
Clinica 0.5.2¶
Changed¶
- [
dwi-preprocessing*
] Rewrite ofdwi-preprocessing*
pipelines using FSL'seddy
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 ofadni-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 byt1-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 imagespet-surface-longitudinal
pipeline: Surface-based longitudinal processing of PET imagescheck-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 oft1-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:¶
- [New]
t1-freesurfer-longitudinal
pipeline: FreeSurfer-based longitudinal processing of T1-weighted MR images [Reuter et al., 2012]. More info in the wiki: https://aramislab.paris.inria.fr/clinica/docs/public/latest/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
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
andstatistics-volume
pipelines
Contact us !¶
- Check for past answers on Clinica Google Group
- Start a discussion on GitHub
- Report an issue on Github