ClinicaDL 1.1.1

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.

ClinicaDL 1.1.0

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.

ClinicaDL 1.0.4

Changed

Core:

• Switch to Poetry to manage production and development requirements.
• Update requirements.
• Improve metrics for multi-class settings.
• Remove NaN values in input data.
• Allow to choose the name of the JSON file produced by extract.
• Improve logs.

Command line:

• Add selection_metrics option in clinicadl train (already available in TOML file).
• Print help if no argument is given.

Fixed

• Fix label code generation
• Remove all occurences of a group in a MAPS when choosing the overwriting option.
• Fix resume when the training.tsv file is empty.

ClinicaDL 1.0.3

ClinicaDL 1.0.3 (release bugfix)

Fixed

• Fix import module for VAE architectures.

ClinicaDL 1.0.2

ClinicaDL 1.0.2

Changed

Core:

• Clinica version dependency.
• Update documentation, with proofreading.
• Change the test for extract.

Fixed

• Use the GPU option on the command line interface.
• Fix the train task when invoking the CLI.
• Remplace the predict arguments passed through the CLI.
• Fix issue when using multiple cohorts.

ClinicaDL 1.0.1

ClinicaDL 1.0.1

Changed

Functionalities:

• extract improve this functionality with more expressive and easy to understand flags.
• Change the test for extract.

Fixed

• Problem when looking for generate module when installing the package with pip.

ClinicaDL 1.0.0

ClinicaDL 1.0.0

Welcome to ClinicaDL 1.0.0 🎉!

This is a new version of ClinicaDL with some major changes in the source code. All the main pipelines
have been refactored. ClinicaDL now used is now working with classes instead of function for easier maintenance
and better scalability. We introduce in this version our new data structure called MAPS to unify ClinicaDL outputs.

This release also include a major command line refactoring with the introduction of Click library.
Major changes in several pipelines interfaces have been implemented. For instance the preprocessing pipeline has been
split. Train pipeline has also been refactored to reduce the number of options. The goal is to make ClinicaDL more easy to use, to maintain,
and adapt the command line to the MAPS.

ClinicaDL aim for more reproducibility: some configuration files are saved in the MAPS to reproduce experiments in the same condition
(with same environnement and same parameters). In addition we added some options to fix the random processes seed and use Pytorch
latest enhancement for a deterministic behavior.

Other improvement and small fix have also been implemented.

⚠️ Be careful, this version breaks the backward compatibility with previous versions. ⚠️

Added

Pipelines:

• New extract pipeline to convert nifti images in Pytorch tensors. This pipeline now saves a preprocessing json file
  with all the information needed for the train pipeline.

Core:

• New folder structure: MAPS (Model Analysis and Processing Structure) for ClinicaDL outputs.
• New class MapsManager for MAPS to ease the interface with the MAPS: launch various tasks such as
  training and prediction, save outputs, read files...
• Other new classes to make ClinicaDL code more scalable: SplitManager, TaskManager, Network...
• Now takes pet-linear images as possible data modality.
• Possibility to fix the seed for a deterministic behavior.

Other:

• New arguments for ROI in random search.

Changed

Pipelines:

• train pipeline has now a new command line. Please see the doc for more information.
• train now accept a TOML configuration file to simplify the command line.
• train resume is now named resume.
• random-search generate is now named random-search
• random-searchnow use TOML configuration file instead of JSON.
• generate pipeline to generate synthetic dataset (random, trivial and Shepp-Logan).
• quality-check pipeline to perform quality check on Clinica t1-linear and t1-volume outputs.

Core:

• Major refactoring of the source code repository organization: now ClinicaDL core
  respects the command line hierarchy as is in Clinica repository.
• Command line: we now use Click instead of Argparse.

Other:

• Console logs enhancement.
• Replace tensorboardx dependency with torch.utils.tensorboard to remove tensorboardx from requirement.
• GitHub repository name is now ClinicaDL and not AD-DL anymore.
• We will now use GitHub discussion instead of Google Group.

Deprecated

Removed

Pipelines:

• clinicadl preprocessing pipelines have been removed. They now have new names (see above).
• clinicadl preprocessing run has now completely been removed. Please use Clinica for preprocessing.
• train_from_json pipeline has been replaced with TOML configuration file.
• clinicadl random-search analysis pipeline has been removed.

Core:

• T1-extensive preprocessing is not supported by ClinicaDL anymore.

Fixed

• Fix multi-class classification.
• Fix classification when only one ROI is given.
• Fix tsvtools when diagnosis column value is not identical to tsv file name.
• Fix clinicadl tsvtool split when n_test is 1.
• Fix ROI when user provides 3D tensor for ROI.
• Fix the use of GPU on a machine with more than on GPU (such a computer cluster).
  ClinicaDL will now select a free GPU that as permission.
• Fix an error where diagnosis column was automatically overwritten
  by the name of the file during split or kfold.

ClinicaDL 0.2.2

ClinicaDL 0.2.2

Added

• New functionality clinicadl random-search analysis to obtain the histogram
  of the balanced accuracy over a random search folder.
• New functionality clinicadl train from_json to train a model with
  parameters defined in a JSON file.
• New functionality clinicadl train resume to resume a prematurely stopped
  training task.
• Possibility to learn the grey matter intensities with the binary
  classification during training, based on t1-volume outputs.
• Refactor code style using Black tool.

Changed

• Previous clinicadl random-search is now clinicadl random-search generate
• Cross-validation and computational arguments of clinicadl random-search generate are now defined in random_search.json.
• Remove tensorboardx dependency.

ClinicaDL 0.2.1

ClinicaDL 0.2.1

Added

• the multi_cohort flag in train allows to train on several CAPS at the same time.

Changed

• clinicadl train roi now allows any ROI defined by a mask.
• Update README.md to avoid duplicates.
• JSON files are added for clinicadl classify and clinicadl tsvtool getlabels|split|kfold

Removed

• Scripts and data related to MedIA publication.

ClinicaDL v0.2.0

ClinicaDL v0.2.0

Added

• New functionality clinica interpret to generate saliency maps linked
  to pretrained models based on groups of individual images.
• New functionality clinicadl random-search to sample random networks from a
  predefined hyperparameter space.
• Slice subparsers for autoencoder/cnn/multicnn to be homogeneous with other
  parsers.
• roi parser has now multicnn option.
• Add generic options to command line: --verbose, --version and
  --logname.

Changed

• Behaviour of clinicadl quality-check t1-volume.
• Simplify clinicadl tsvtools behaviour when using getlabels, split and
  analysis.
• Update documentation.

Fixed

• Fix broken file when running preprocessing in t1-extensive.