Clinica

Fixed

* Fix t1-volume quality-check empty tsv issue,
* Fix bug with adapt pipeline,
* Fix `predict —-overwrite` issue,


Changed

* Remove Clinica dependency
* Change MapsManager architecture by adding more Callbacks,
* Update python to v3.11 and pytorch to v2.0,

New

* Add missing methods in models classes,
* Add `--save_all_models` option to save models weights at each epochs,
* Add `--skip_leak_check` option to skip data leakage check,
* Add `--adaptive_learning_rate` option,
* Add `prepare-data-from-bids` pipeline to extract tensor from bids to caps,
* Add dti modality,
* Add `hugging-face push/pull` pipelines to share models on HuggingFace,
* Add confidence intervals and metrics

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.

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

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`.

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 `interpret`command.
* 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.