Clinicadl Versions Save

ClinicaDL 1.6.1

Fixed

• Fix sorting particpants sessions with 2 digit,
• Fix interpret —-save_nifti issue,
• Fix BIDS file format for pet,

Changed

• Change 2 digits session label to 3 digits,
• Change black and isort for ruff and codespell,
• Update type hint and docstring,

New

• Add --fsdp option
• Add --valid_longitudinal option to allow the validation on longitudinal data,

ClinicaDL 1.5.1

Fixed

• Fix retrocompatibility for new option in maps.json

Changed

• Change MapsManager architecture by adding Callbacks

New

• Add --fully_sharded_data_parallelism option
• Add --emisions_calculator option with codecarbon
• Add the semi-supervised domain adaptation network proposed for the MICCAI DART workshop.

ClinicaDL 1.5.0

Fixed

• Fix adapt command

Changed

• SSIM is now executed on GPU when possible

New

• Add new command generate artifacts to generate noise/contract/motion
• Add options for data augmentation
• Add fine-tuning option
• Add --amp for automatic mixed precision
• Add --track_exp option to track your parameters during training with MLflow or WandB

Fixed

• Fix --diagnoses and --merged_tsv option bug in clinicadl get-labels
• Fix Pathlib bugs
• Fix get_tsv_paths function bug.
• Fix a bug for which it was impossible to use predict without specifying the splits and selection metrics.

Changed

• Changed default batch size to 8 for clinicadl predict
• Changed VAEs main class

New

• Add --n_proc option in clinicadl generate pipelines for parallelization.
• Add --split to clinicadl predict
• Add new VAE networks.
• Add pytorch function to summarize
• Add --size_reduction and --size_reduction_factor options to clinicadl train, clinicadl predict and clinicadl interpret.
• Add SSIM2D, SSIM3D metrics for VAE.
• Add --save_latent_space option to clinicadl train and clinicadl predict.
• Add clinicadl generate trvial_motion
• Add Data augmentation with torchio

ClinicaDL 1.3.1

Fixed

• Fix TypeError when running ClinicaDL.
• Fix --extract_json option bug in clinicadl prepare-data.
• Fix clinicadl tsvtools get-labels error finding clinica iotools missing-modalities output.

Changed

• Changed clinicadl tsvtools get-labels output directory.

New

• Add --caps_directory option in clinicadl tsvtools get-labels.

ClinicaDL 1.3.0

New

• Add new command quality-check pet-linear.
• Add new command generate hypometabolic.
• Add new network architecture: Resnet3D and SqueezeExcitationCNN.
• Add flair-linear modality for prepare-data command.
• Add pytorch profiler.
• Add --save_nifti option for interpretcommand.
• Add --output_dir argument for tsvtools get-labels command

Changed

** Core: **

• Transition from os to pathlib.
• Update data CI.
• Improve maps_manager.
• Change --acq_label option for --tracer.
• Update tutorial.

ClinicaDL 1.2.0

Changed

** Core: **

• Add ClinicaDL installation with pipx.
• Improve logging.
• Add method argument to the interpret command to choose between the new Grad-CAM method and the gradient method.
• Change extract command to prepare-data.
• Change output of get-labels, split and kfold commands to one TSV per split instead of one per label.
• Change tsvtool command to tsvtools.
• Change tsvtools getlabels command to tsvtools get-labels and remove the progression column in the TSV output.
• Add new commands: tsvtools get-progression, tsvtools get-metadata, tsvtools prepare-experiment (split + kfold), and tsvtools adapt.
• Update data CI.
• Add a new model for quality check

Fixed

• Fix quality-check t1-linear

Changed

** Core: **

• Dependencies versions were updated in order to support Python equal or greater than 3.8.
• Security updates for some dependencies.
• Include the --save_tensor and --save_nifty options into the predict sub-command (before save_tensor was also subcommand`).
• Update some paper references in the documentation.
• Add a description for the available models.
• Add the flag --model_layers to the clinicadl train list_models subcommad to visualize the model layers.

Fixed

• Fix bug when using the clinicadl train list_models command.

Changed

Core:

• Add new VAE models for training.
• Add multiprocessing for the extract task.
• Add tests to validate resume and quality-check functionalities.
• Update minimal version for first level dependencies: clinica, scikit-learn, scikit-image.
• Add a new Makefile to the root of the repository in order to facilitate sysadmin frequent tasks. The CI script was also modified.

Command line:

• Update of the train command line: now all actions related to training (resume, list models, tasks…) are sub-commands of the command clinicadl train. Task is now a sub-command, and not an argument.
• Add command to list the available models for the training task and the details of each model.
• Add an option to the command save-tensor to save the reconstruction outputs as nifti files.
• Add command clinicadl train from_json to train again the same experiment from a JSON file generated by ClinicaDL.

Fixed

• Allow the user to choose the optimizer and the metric independently of the performed task.
• Logger does not display output according to the --verbose option during the training tasks. This behavior is fixed.
• Behavior of resume was changed.
• Reader to request BIDS/CAPS datasets changed its interface in the recent version of Clinica (>=0.5.4). Code using these functions was adapted.
• Exceptions raised are now more specific and detailed.
• Documentation was updated.