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Releases: aramis-lab/clinicadl

ClinicaDL v1.6.1

05 Apr 11:42
eb08045
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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 v1.6.0

16 Feb 17:56
c6177e4
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pyproject release (#530)

ClinicaDL v1.5.1

07 Oct 14:01
b2f145d
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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 v1.5.0

12 Sep 12:29
a1464c5
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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

ClinicaDL v1.4.0

09 Jun 13:42
dde6437
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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

Release ClinicaDL 1.3.1

15 May 15:49
15198d6
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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.

Release ClinicaDL v1.3.0

13 Apr 12:15
22b49c6
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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

15 Feb 15:39
43f7056
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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

ClinicaDL 1.1.1

28 Jul 14:49
8290e29
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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

10 Feb 11:42
cd6decf
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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.