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Recent Releases of clinica

clinica - Release 0.10.1

Fixed

  • [IOTools] Fix merge-tsv tool and its caps option (PR #1535)
  • [Dependencies] Update dependencies and perform associated fixes (PR #1531)

- Python
Published by AliceJoubert 7 months ago

clinica - Release 0.10.0

Fixed

  • [IOTools] Fix broken import of bids.dataset module (PR #1484)
  • [IOTools] Center-Nifti now runs by default on T1 as it was expected (PR #1418)
  • [DWI] Fix broken import of bids.dataset module (PR #1523)
  • [Converters] GENFI : Fix validation of optional path to clinical data (PR #1513)
  • [Pipelines] Fix SPM standalone version check (PR #1488)

Enhanced

  • [Pipelines] Search for SPM standalone version is not hardcoded to SPM12 anymore (PR #1490)
  • Improve architecture for BIDS and CAPS datasets logic (PR #1453)

Added

  • [IOTools] When using Center-Nifti it is now possible to choose the centering threshold (PR #1433)
  • [DOC] Warning about SPM standalone version (PR #1496)
  • [T1Volume] Skip processed visits (PR #1403)
  • [AIBL-to-BIDS] Now has a json constructor based on dicoms to retrieve information required to fit BIDS specifications (PR #1500)

Removed

  • [Pipelines] Remove interactivity when centering images is required by the pipeline (PET-Volume, T1-Volume, PET-Surface, T1-Freesurfer) (PR #1419)

- Python
Published by AliceJoubert 9 months ago

clinica - Release 0.9.4

Fixed

  • [PET] Fix query pattern when a tracer is specified but not the reconstruction method (see PR #1470)
  • [Converters] Fix type mismatch in clinica.iotools.bids_utils (see PR #1376)

- Python
Published by NicolasGensollen 11 months ago

clinica - Release 0.9.3

Fixed

  • [PETLinear] Fix the SUVR normalization step (see PR #1348)

- Python
Published by NicolasGensollen over 1 year ago

clinica - Release 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)

- Python
Published by NicolasGensollen over 1 year ago

clinica - Release 0.9.1

Fixed

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

- Python
Published by NicolasGensollen over 1 year ago

clinica - Release 0.9.0

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 #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)

- Python
Published by NicolasGensollen over 1 year ago

clinica - Release 0.8.4

Fixed

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

- Python
Published by NicolasGensollen over 1 year ago

clinica - Release 0.8.3

Fixed

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

- Python
Published by NicolasGensollen over 1 year ago

clinica - Release 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)

- Python
Published by NicolasGensollen over 1 year ago

clinica - Release 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)

- Python
Published by NicolasGensollen almost 2 years ago

clinica - Release 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)

- Python
Published by NicolasGensollen almost 2 years ago

clinica - Release 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)

- Python
Published by NicolasGensollen about 2 years ago

clinica - Release 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)

- Python
Published by NicolasGensollen over 2 years ago

clinica - Release 0.7.5

Enhanced

  • [Converters] Improvements to GENFI to BIDS converter
  • [Converters] Improvements to Oasis3 to BIDS converter
  • [Pipelines] Add the possibility to specify a random seed to be used with ANTs

Fixed

  • [Converters] GENFI to BIDS various fixes
  • [Converters] Fix ADNI to BIDS issue with unsupported visit code "uns1"
  • [MachineLearning] Fix bug in CLI of pipeline machinelearning-prepare-spatial-svm

- Python
Published by NicolasGensollen over 2 years ago

clinica - Release 0.7.4

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

- Python
Published by NicolasGensollen almost 3 years ago

clinica - Release v0.7.3

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 createsubssess_list
  • [IOTools] Fix voxtoworldspacemethod_1

- Python
Published by NicolasGensollen over 3 years ago

clinica - Release v0.7.2

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

- Python
Published by omar-rifai over 3 years ago

clinica - Release v0.7.1

Added

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

Changed

  • [Core] Enable parallelelization when grabbing files

Fixed

  • [Converters] Fix several warnings

- Python
Published by omar-rifai over 3 years ago

clinica - Release v0.7.0

New

  • [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

- Python
Published by omar-rifai almost 4 years ago

clinica - 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

- Python
Published by omar-rifai almost 4 years ago

clinica - 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)

- Python
Published by ghisvail almost 4 years ago

clinica - Clinica v.0.5.5

Hotfix

  • Fix pet-linear infinite loop problem

- Python
Published by omar-rifai about 4 years ago

clinica - 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

- Python
Published by omar-rifai about 4 years ago

clinica - 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 OASIS3tobids instructions for conversion
  • [StatisticsSurface] Fix type in covariate argument
  • [StatisticsVolume] Fix bug in feature argument

- Python
Published by omar-rifai about 4 years ago

clinica - 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

- Python
Published by omar-rifai over 4 years ago

clinica - 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

- Python
Published by omar-rifai over 4 years ago

clinica - 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 getdata() by getfdata() 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 writescantsv
  • [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

- Python
Published by omar-rifai over 4 years ago

clinica - 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 getdata() by getfdata() 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 writescantsv
  • [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

- Python
Published by omar-rifai over 4 years ago

clinica - 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

- Python
Published by omar-rifai almost 5 years ago

clinica - 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.

- Python
Published by mdiazmel almost 5 years ago

clinica - 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 DataDictionaryNIFD.xlsx file when using NIFD2BIDS.

- Python
Published by mdiazmel about 5 years ago

clinica - 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/T1FreeSurferLongitudinal/
  • [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/clinicapipelinefmri_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

- Python
Published by mdiazmel over 5 years ago

clinica - Clinica 0.3.5

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: http://www.clinica.run/doc/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.

- Python
Published by mdiazmel over 5 years ago

clinica - Clinica 0.3.6

Changes

Clinica Core:

  • [Change] Pip is the main way to install Clinica. Conda packages are not available for the new versions.
  • [Update] Set the minimalSet 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-2-bids converter now handles new version of clinical data.
  • [Update] The oasis-2-bids converter now uses NiBabel instead of FreeSurfer to convert OASIS dataset.

- Python
Published by mdiazmel over 5 years ago

clinica - Clinica 0.3.4

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

- Python
Published by mdiazmel almost 6 years ago

clinica - Clinica 0.3.3

Changes

Clinica Core:

  • [New] Use PEP8 Speaks tool for PEP8 checks.
  • [Improvement] Improve Jinja2 template. ## Pipelines:
  • [New] t1-linear - Affine registration of T1w images to the MNI standard space. More info on the Wiki: http://www.clinica.run/doc/Pipelines/T1_Linear .
  • [New] statistics-volume and (experimental) statistics-volume-correction - Volume-based mass-univariate analysis with SPM. More info on the Wiki: http://www.clinica.run/doc/Pipelines/Stats_Volume .
  • [Fix] Error for pet-surface pipeline with unzipped files (Issue #68).
  • [Improvement] Improve error message in pet-surface when metadata are missing in JSON file (Issue #69).
  • [Fix] Prevent Clinica from running PET pipelines on 4D volumes (Issue #70).
  • [Fix] Display clear error message when trying to create a DARTEL template with one image (Issue #74).
  • [Fix] Fix bug where CAPS outputs for t1-freesurfer pipeline were not saved (Google Groups). ## Converters:
  • [Fix] Fix wrong path for BIDS FLAIR MR image, missing JSON files for DWI, error when generating paths for AV45 and Florbetaben PET images for adni-2-bids(Issue #50).
  • [New] Add new fields to clinical data in adni-2-bids e.g. Clinical Dementia Rating Scale (CDR), Montreal Cognitive Assessment (MOCA). The full list is located in the file clinica/iotools/data/clinical_specifications_adni.xlsx.
  • [Improvement] General improvements for adni-2-bids are detailed in PR #55 and merged in PR #64.

- Python
Published by mdiazmel almost 6 years ago

clinica - Version 0.3.2

Changes

Clinica Core:

  • [Enh] Harmonize how working directory is handled in Clinica.
  • [New] For any pipeline, delete automatically working directory if not specified in the CLI.
  • [Fix] Catch case when no image is given to a pipeline (e.g. because they were already processed in CAPS directory).
  • [Enh] Harmonize use of pipeline parameters and how they are handled. ## Pipelines:
  • [Change] Pipeline classes associated to t1-volume and t1-volume-existing-template command lines are removed. They are simply replaced by successive calls of t1-volume* sub-pipelines.
  • [New] For t1-freesurfer, display failed images when an error occurs during the execution of the pipeline.
  • [New] For t1-freesurfer, add --overwrite-outputs flag. When used, images already run in CAPS directory will rewritten. Otherwise, they will be skipped before the execution of the pipeline.
  • [Fix] Remove mentions of modulation in t1-volume-parcellation arguments (modulated images are always chosen).
  • [Fix] Remove --smooth flag in t1-volume-tissue-segmentation (should not exist).
  • Enh Remove discrepancy between CLI flag and pipeline parameter.

- Python
Published by mdiazmel about 6 years ago

clinica - Version 0.3.1

Changes

Clinica Core:

  • [Fix] Remove the double equal from conda environment file, to be compatible with conda > 4.7
  • [New] Add clinica_file_reader / clinica_group_reader functions to read input files for Clinica
  • [New] Add ux.py to centralize output message for each pipeline (currently used in t1-freesurfer pipeline)
  • [Enh] Improve verifications in check_bids_folder / check_caps_folder
  • [Enh] Improve how Clinica handles SPM/SPM-Standalone on Mac/Linux and how Clinica extracts TPM file.
  • [Enh] Replace duplicated code by calls of check_spm, check_cat12 and check_environment function
  • [Enh] Remove obsolete functions ## Pipelines:
  • [Fix] Check volume locations in t1-freesurfer and t1-volume pipelines
    • For t1-freesurfer, this check is useful if the user plans to use pet-surface afterwards.
    • For t1-volume, this check is important since SPM Segment() expects centers of T1w images to be closed to 0.
  • [Fix] Check relative volume locations in pet-surface and pet-volume pipelines. In these pipelines, SPM Coregister() method is used to register T1w and PET images. However, if the centers of these images are far from each other, this registration may fail
  • [Enh] Rewrite build_input_node method for all pipelines
  • [Enh] Harmonize exception handling when missing or duplicated BIDS/CAPS files are present for all pipelines
  • [Enh] Change how to find NaN values in images
  • [Fix] t1-freesurfer: Fix the sending of argument for -raa/--recon_all_args flag ## IOTools:
  • [New] Add center-nifti IOTool to center NIfTI files of a BIDS directory. This tool is mainly used when SPM is not able to segment some T1w images because the centers of these volumes are not aligned with the origin of the world coordinate system. By default, only problematic images are converted. The rest of the images are also copied to the new BIDS directory, but left untouched.

- Python
Published by mdiazmel over 6 years ago

clinica - Version 0.3.0

Changes

Clinica Core:

  • [Improvement] General improvements include better error handling/message when executing Clinica (missing dependency, BIDS/CAPS handling, typos, warning messages).
  • [Fix] After fixing "Assuming non interactive session since isatty found missing" for Clinica 0.2.2, Clinica became too verbose when running a pipeline (Issue #7). An alternative bugfix was used.
  • [New] Add timeout when asking if pipeline starts even though disks are full
  • [New] Add timeout when asking user for n_procs
  • [New] Detect if extra flags are given and if -v is used after clinica {run|iotools|convert}
  • [New] Add warning message if PYTHONPATH is not empty (should avoid this situation)

Pipelines:

  • [New] dwi-connectome pipeline: Construction of structural connectome with computation of fiber orientation distributions, tractogram and connectome. More info on the Wiki: http://www.clinica.run/doc/Pipelines/DWI_Connectome
  • [Change] t1-freesurfer pipeline was rewritten. It includes a complete refactoring and:
    • The pipeline is now executed in the working directory and outputs without errors from FreeSurfer or Nipype are now copied from the working directory to the CAPS folder;
    • the symbolic links (e.g. fsaverage) are not present in the CAPS folder anymore;
    • If Clinica fails on some images, it detects & displays the subjects who failed.
  • [Change] The TSV files generated by the t1-freesurfer* pipelines are now ordered in two columns (name, value)- [Fix] Fix parallelization in t1-volume-tissue-segmentation and t1-volume-existing-template pipelines: if SPM failed on an image, Clinica did not manage to save successful results of other images in CAPS directory
  • [Fix] Remove atlas statistics generation in t1-volume-dartel2mni pipeline
  • [Fix] Check the presence of CAT12 in volume pipelines. Otherwise, the pipeline failed when trying to generate statistics for atlases part of the CAT12 toolbox.
  • [Fix] Include Matlab files from ‘pipelines’ folder when using the user installation (i.e. without pip -e .). Otherwise, pet-volume pipeline failed.
  • [Fix] Sort diagnosis list to avoid mixing labels when testing for ML modules.
  • [Update] Edit path to search Tissue Probability Map in SPM standalone.
  • [Update] Remove several obsolete functions and workflows.

Converters:

  • [Update] The adni-2-bids converter now includes ADNI3 and new modalities (fMRI, PET data)
  • [New] nifd-2-bids converter: You can now convert the NIFD dataset (http://4rtni-ftldni.ini.usc.edu) into BIDS. More info on the Wiki: http://www.clinica.run/doc/DatabasesToBIDS/#nifd-to-bids
  • [Fix] Fix age in sessions.tsv file for adni-2-bids (the age was the same across sessions)
  • [New] Compute age from date of birth and date of exam for aibl-2-bids
  • [Improvement] Deduce missing examination dates in aibl-2-bids
  • [Fix] Remove duplicates in oasis-2-bids converter

IOTools:

  • [Fix] Fix missing modalities bug where FLAIR and T1w could be miscounted
  • [Improvement] Improve error message for iotools commands (e.g. when `-tsv is not a file, when BIDS parameter is not a folder)

- Python
Published by alexandreroutier over 6 years ago

clinica - Version 0.2.2

Changes

  • [CI] Continuous integration updated with Jenkins following GitHub migration
  • [Update] adni-to-bids converter improvements: multiprocessing, less crashes, better display
  • [Update] Test folder for CI is reorganized
  • [Fix] pet-volume: tsv needed for partial volume correction can now be used
  • [Fix] Bug where SPM Standalone could not be used in pipelines is now fixed
  • [Fix] Bug in aibl-to-bids converter that could cause Clinica to crash is now fixed
  • [Fix] In t1-volume-existing-template, a better check is carried out on the group name
  • [Fix] The message "Assuming non interactive session since isatty found missing" has disappeared
  • [New] Clinica now handles cross sectional dataset by automatically proposing the user to convert it into a longitudinal dataset
  • [New] Implementation of a new multiclassification algorithm
  • [New] Improvement of information on crash display
  • [New] No Warning messages are displayed
  • [New] Python dependencies are now freezed to ensure non regression

- Python
Published by mdiazmel over 6 years ago

clinica - Version 0.2.1

Changes

  • [Fix] Fix bug in the aibl-to-bids converter.
  • [Improvement] Improvement of the converter oasis-to-bids
  • [Fix] Include duecredit as dependency.

- Python
Published by alexandreroutier almost 7 years ago

clinica - Version 0.2.0 Beta 3 (pre-release)

Changes

  • Pre-release version (0.2.0 Beta 3).
  • Full changes description with the final release.

- Python
Published by alexandreroutier almost 7 years ago

clinica - Version 0.2.0 Beta 2 (pre-release)

Changes

  • Pre-release version (0.2.0 Beta 2).
  • Full changes description with the final release.

- Python
Published by alexandreroutier almost 7 years ago

clinica - Version 0.1.3

Changes

  • Unit testing in macOS

- Python
Published by alexandreroutier almost 7 years ago

clinica - Version 0.1.2

Changes

  • CI running on macOS and Linux

  • Tarball file available to download

- Python
Published by alexandreroutier almost 7 years ago

clinica - Version 0.2.0

Changes

Clinica Core:

  • [Update] Clinica is now using Python 3.6.0 & Nipype 1.1.2.
  • [New] A CI framework is set up for Clinica.
  • [Improvement] General improvements include better error handling/message when executing Clinica.
  • [New] Clinica checks if there is sufficient space before running a pipeline.
  • [New] Clinica ensures that multithreading is used before running a pipeline, and warns the user otherwise.
  • [Fix] Relative path in command line now works properly.
  • [New] The Clinica project is now PEP8 compliant.

Pipelines:

  • [New] machinelearning-prepare-spatial-svm pipeline: Prepare input data for spatially regularized SVM [Cuingnet et al, 2013]. More info on the Wiki: http://www.clinica.run/doc/Pipelines/MachineLearning_PrepareSVM/
  • [New] fmri-preprocessing pipeline: fMRI pre-processing with slice timing and motion correction, brain extraction and spatial normalization. More info on the Wiki: http://www.clinica.run/doc/Pipelines/fMRI_Preprocessing/
  • [Change] The dwi-processing-noddi (and its prerequisites dwi-preprocessing-multi-shell) is removed from the Clinica software as we will not actively maintain it. It is now on a separate repository: https://github.com/aramis-lab/clinicapipelinenoddi
  • [Fix] t1-freesurfer now handles FreeSurfer 6.0.0.
  • [Change] New pipeline names :
    • t1-freesurfer-cross-sectional becomes t1-freesurfer;
    • t1-spm-* pipelines become t1-volume-*. In particular, t1-spm-full-prep is now t1-volume and t1-volume-existing-dartel is now t1-volume-existing-template;
    • dwi-preprocessing-using-phasediff-fieldmap is now dwi-preprocessing-using-fieldmap;
    • dwi-processing-dti pipeline becomes dwi-dti;
    • pet-preprocessing-volume pipeline becomes pet-volume.

Converters:

[New] The ADNI-2-BIDS converter now includes the diffusion MRI and FLAIR sequences.

IOTools:

[Fix] Fix merge-tsv command line when no path was given to the TSV file. [New] The merge-tsv can now parse TSV files from CAPS. Currently, it only supports the t1-volume and pet-volume pipelines.

- Python
Published by alexandreroutier almost 7 years ago