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

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.

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.

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

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.

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] (All pipelines) Remove discrepancy between CLI flag and pipeline parameter.

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.

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)