diff --git a/README.md b/README.md index 4d1dc6df88ee20de0e43be3b49e46b4ff8e412ba..b5fe947534f7d52f9bf42505a82ff6a2a91b18dc 100644 --- a/README.md +++ b/README.md @@ -1,90 +1,70 @@ --- license: mit language: -- en + - en datasets: -- mathpluscode/ACDC + - mathpluscode/ACDC tags: -- medical -- cardiac -- MRI -- foundation model -- MAE + - medical + - cardiac + - MRI + - foundation model + - MAE --- # CineMA - A Foundation Model for Cine Cardiac Magnetic Resonance Images 🎥🫀 -This repository contains the weights for **CineMA**, a foundation model for **Cine** cardiac magnetic resonance (CMR) -imaging based on **M**asked-**A**utoencoder. The model was pre-trained on over 74,000 pairs of short-axis and long-axis -cine CMR images from the UK Biobank. +**CineMA** is a foundation model for **Cine** cardiac magnetic resonance (CMR) imaging based on +**M**asked-**A**utoencoder. CineMA has been pre-trained on UK Biobank data and fine-tuned on multiple clinically +relevant tasks such as ventricle and myocaridum segmentation, ejection fraction (EF) regression, cardiovascular disease +(CVD) detection and classification, and mid-valve plane and apical landmark localization. The model has been evaluated +on multiple datasets, including [ACDC](https://www.creatis.insa-lyon.fr/Challenge/acdc/), +[M&Ms](https://www.ub.edu/mnms/), [M&Ms2](https://www.ub.edu/mnms-2/), +[Kaggle](https://www.kaggle.com/c/second-annual-data-science-bowl/data), +[Rescan](https://www.ahajournals.org/doi/full/10.1161/CIRCIMAGING.119.009214), and +[Landmark](https://pubs.rsna.org/doi/10.1148/ryai.2021200197), etc. -CineMA was evaluated across a diverse range of clinically relevant downstream tasks, including - -- Ventricle and myocardium segmentation -- Cardiovascular disease (CVD) detection and classification -- Patient sex classification -- CMR machine vendor classification -- Ejection fraction (EF) regression -- Patient body mass index (BMI) regression -- Patient age regression -- Mid-ventricular and apical landmark localization - -These tasks were studied across multiple datasets: - -- [ACDC](https://www.creatis.insa-lyon.fr/Challenge/acdc/) -- [M&Ms](https://www.ub.edu/mnms/) -- [M&Ms2](https://www.ub.edu/mnms-2/) -- [Kaggle](https://www.kaggle.com/c/second-annual-data-science-bowl/data) -- [Rescan](https://www.ahajournals.org/doi/full/10.1161/CIRCIMAGING.119.009214) -- [Landmark](https://pubs.rsna.org/doi/10.1148/ryai.2021200197) - -Compared to convolutional neural network baselines such as UNet and ResNet, CineMA demonstrated superior or comparable -performance, especially in sample efficiency and generalization to out-of-distribution data not seen during pretraining -or fine-tuning. - -By releasing the model weights and code for pretraining, fine-tuning, and inference, CineMA aims to lower the barrier to -entry for cardiac imaging research, foster reproducibility, and encourage broader adoption across institutions. - -➡️ **Manuscript:** [TBD](https://arxiv.org/) +➡️ **Manuscript:** Coming soon. ➡️ **Code:** [mathpluscode/CineMA](https://github.com/mathpluscode/CineMA) ## Fine-tuned CineMA Models -The filenames of fine-tuned model weights follow the convention of `finetuned//__.safetensors` -where number 0, 1, and 2 correspond to the different training seeds. +The filenames of fine-tuned model weights follow the convention of +`finetuned//_/__.safetensors` where number 0, 1, and 2 correspond to the different +training seeds. Check the "Inference Example" column to see example inference scripts using these trained models. -| Training Task | Training Data | Input View | Input Timeframes | Model Weights and Configurations | Inference Example | -| ----------------------------------------------- | ------------- | ---------- | ---------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------ | -| Ventricle and myocardium segmentation | ACDC | SAX | 1 | [finetuned/segmentation/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/acdc_sax_0.safetensors)
[finetuned/segmentation/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/acdc_sax_1.safetensors)
[finetuned/segmentation/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/acdc_sax_2.safetensors)
[finetuned/segmentation/sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/sax.yaml) | [segmentation_sax.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_sax.py) | -| Ventricle and myocardium segmentation | M&Ms | SAX | 1 | [finetuned/segmentation/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms_sax_0.safetensors)
[finetuned/segmentation/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms_sax_1.safetensors)
[finetuned/segmentation/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms_sax_2.safetensors)
[finetuned/segmentation/sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/sax.yaml) | [segmentation_sax.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_sax.py) | -| Ventricle and myocardium segmentation | M&Ms2 | SAX | 1 | [finetuned/segmentation/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_sax_0.safetensors)
[finetuned/segmentation/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_sax_1.safetensors)
[finetuned/segmentation/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_sax_2.safetensors)
[finetuned/segmentation/sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/sax.yaml) | [segmentation_sax.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_sax.py) | -| Ventricle and myocardium segmentation | M&Ms2 | LAX 4C | 1 | [finetuned/segmentation/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_lax_4c_0.safetensors)
[finetuned/segmentation/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_lax_4c_1.safetensors)
[finetuned/segmentation/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_lax_4c_2.safetensors)
[finetuned/segmentation/lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/lax_4c.yaml) | [segmentation_lax_4c.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_lax_4c.py) | -| CVD classification | ACDC | SAX | 2 (ED and ES) | [finetuned/classification_cvd/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax_0.safetensors)
[finetuned/classification_cvd/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax_1.safetensors)
[finetuned/classification_cvd/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax_2.safetensors)
[finetuned/classification_cvd/acdc_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | -| CVD classification | M&Ms | SAX | 2 (ED and ES) | [finetuned/classification_cvd/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax_0.safetensors)
[finetuned/classification_cvd/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax_1.safetensors)
[finetuned/classification_cvd/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax_2.safetensors)
[finetuned/classification_cvd/mnms_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | -| CVD classification | M&Ms2 | SAX | 2 (ED and ES) | [finetuned/classification_cvd/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax_0.safetensors)
[finetuned/classification_cvd/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax_1.safetensors)
[finetuned/classification_cvd/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax_2.safetensors)
[finetuned/classification_cvd/mnms2_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | -| CVD classification | M&Ms2 | LAX 4C | 2 (ED and ES) | [finetuned/classification_cvd/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c_0.safetensors)
[finetuned/classification_cvd/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c_1.safetensors)
[finetuned/classification_cvd/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c_2.safetensors)
[finetuned/classification_cvd/mnms2_lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | -| Patient sex classification | M&Ms | SAX | 2 (ED and ES) | [finetuned/classification_sex/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax_0.safetensors)
[finetuned/classification_sex/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax_1.safetensors)
[finetuned/classification_sex/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax_2.safetensors)
[finetuned/classification_sex/mnms_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax.yaml) | [classification_sex.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_sex.py) | -| CMR machine vendor classification | M&Ms2 | SAX | 2 (ED and ES) | [finetuned/classification_vendor/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax_0.safetensors)
[finetuned/classification_vendor/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax_1.safetensors)
[finetuned/classification_vendor/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax_2.safetensors)
[finetuned/classification_vendor/mnms2_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax.yaml) | [classification_vendor.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_vendor.py) | -| CMR machine vendor classification | M&Ms2 | LAX 4C | 2 (ED and ES) | [finetuned/classification_vendor/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c_0.safetensors)
[finetuned/classification_vendor/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c_1.safetensors)
[finetuned/classification_vendor/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c_2.safetensors)
[finetuned/classification_vendor/mnms2_lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c.yaml) | [classification_vendor.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_vendor.py) | -| EF regression | ACDC | SAX | 2 (ED and ES) | [finetuned/regression_ef/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax_0.safetensors)
[finetuned/regression_ef/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax_1.safetensors)
[finetuned/regression_ef/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax_2.safetensors)
[finetuned/regression_ef/acdc_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | -| EF regression | M&Ms | SAX | 2 (ED and ES) | [finetuned/regression_ef/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax_0.safetensors)
[finetuned/regression_ef/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax_1.safetensors)
[finetuned/regression_ef/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax_2.safetensors)
[finetuned/regression_ef/mnms_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | -| EF regression | M&Ms2 | SAX | 2 (ED and ES) | [finetuned/regression_ef/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax_0.safetensors)
[finetuned/regression_ef/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax_1.safetensors)
[finetuned/regression_ef/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax_2.safetensors)
[finetuned/regression_ef/mnms2_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | -| EF regression | M&Ms2 | LAX 4C | 2 (ED and ES) | [finetuned/regression_ef/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c_0.safetensors)
[finetuned/regression_ef/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c_1.safetensors)
[finetuned/regression_ef/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c_2.safetensors)
[finetuned/regression_ef/mnms2_lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | -| Patient BMI regression | ACDC | SAX | 2 (ED and ES) | [finetuned/regression_bmi/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax_0.safetensors)
[finetuned/regression_bmi/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax_1.safetensors)
[finetuned/regression_bmi/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax_2.safetensors)
[finetuned/regression_bmi/acdc_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax.yaml) | [regression_bmi.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_bmi.py) | -| Patient age regression | M&Ms | SAX | 2 (ED and ES) | [finetuned/regression_age/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax_0.safetensors)
[finetuned/regression_age/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax_1.safetensors)
[finetuned/regression_age/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax_2.safetensors)
[finetuned/regression_age/mnms_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax.yaml) | [regression_age.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_age.py) | -| Landmark localization by heatmap regression | Landmark | LAX 2C | 1 | [finetuned/landmark_heatmap/lax_2c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c_0.safetensors)
[finetuned/landmark_heatmap/lax_2c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c_1.safetensors)
[finetuned/landmark_heatmap/lax_2c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c_2.safetensors)
[finetuned/landmark_heatmap/lax_2c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c.yaml) | [landmark_heatmap.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_heatmap.py) | -| Landmark localization by heatmap regression | Landmark | LAX 4C | 1 | [finetuned/landmark_heatmap/lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c_0.safetensors)
[finetuned/landmark_heatmap/lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c_1.safetensors)
[finetuned/landmark_heatmap/lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c_2.safetensors)
[finetuned/landmark_heatmap/lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c.yaml) | [landmark_heatmap.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_heatmap.py) | -| Landmark localization by coordinates regression | Landmark | LAX 2C | 1 | [finetuned/landmark_coordinate/lax_2c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c_0.safetensors)
[finetuned/landmark_coordinate/lax_2c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c_1.safetensors)
[finetuned/landmark_coordinate/lax_2c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c_2.safetensors)
[finetuned/landmark_coordinate/lax_2c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c.yaml) | [landmark_coordinate.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_coordinate.py) | -| Landmark localization by coordinates regression | Landmark | LAX 4C | 1 | [finetuned/landmark_coordinate/lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c_0.safetensors)
[finetuned/landmark_coordinate/lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c_1.safetensors)
[finetuned/landmark_coordinate/lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c_2.safetensors)
[finetuned/landmark_coordinate/lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c.yaml) | [landmark_coordinate.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_coordinate.py) | +| Training Task | Training Data | Input View | Input Timeframes | Model Weights and Configurations | Inference Example | +| ----------------------------------------------- | ------------- | ---------- | ---------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------ | +| Ventricle and myocardium segmentation | ACDC | SAX | 1 | [finetuned/segmentation/acdc_sax/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/acdc_sax/acdc_sax_0.safetensors)
[finetuned/segmentation/acdc_sax/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/acdc_sax/acdc_sax_1.safetensors)
[finetuned/segmentation/acdc_sax/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/acdc_sax/acdc_sax_2.safetensors)
[finetuned/segmentation/acdc_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/acdc_sax/config.yaml) | [segmentation_sax.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_sax.py) | +| Ventricle and myocardium segmentation | M&Ms | SAX | 1 | [finetuned/segmentation/mnms_sax/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms_sax/mnms_sax_0.safetensors)
[finetuned/segmentation/mnms_sax/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms_sax/mnms_sax_1.safetensors)
[finetuned/segmentation/mnms_sax/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms_sax/mnms_sax_2.safetensors)
[finetuned/segmentation/mnms_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms_sax/config.yaml) | [segmentation_sax.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_sax.py) | +| Ventricle and myocardium segmentation | M&Ms2 | SAX | 1 | [finetuned/segmentation/mnms2_sax/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_sax/mnms2_sax_0.safetensors)
[finetuned/segmentation/mnms2_sax/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_sax/mnms2_sax_1.safetensors)
[finetuned/segmentation/mnms2_sax/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_sax/mnms2_sax_2.safetensors)
[finetuned/segmentation/mnms2_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_sax/config.yaml) | [segmentation_sax.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_sax.py) | +| Ventricle and myocardium segmentation | M&Ms2 | LAX 4C | 1 | [finetuned/segmentation/mnms2_lax_4c/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_lax_4c/mnms2_lax_4c_0.safetensors)
[finetuned/segmentation/mnms2_lax_4c/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_lax_4c/mnms2_lax_4c_1.safetensors)
[finetuned/segmentation/mnms2_lax_4c/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_lax_4c/mnms2_lax_4c_2.safetensors)
[finetuned/segmentation/mnms2_lax_4c/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_lax_4c/config.yaml) | [segmentation_lax_4c.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_lax_4c.py) | +| CVD classification | ACDC | SAX | 2 (ED and ES) | [finetuned/classification_cvd/acdc_sax/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax/acdc_sax_0.safetensors)
[finetuned/classification_cvd/acdc_sax/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax/acdc_sax_1.safetensors)
[finetuned/classification_cvd/acdc_sax/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax/acdc_sax_2.safetensors)
[finetuned/classification_cvd/acdc_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax/config.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | +| CVD classification | M&Ms | SAX | 2 (ED and ES) | [finetuned/classification_cvd/mnms_sax/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax/mnms_sax_0.safetensors)
[finetuned/classification_cvd/mnms_sax/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax/mnms_sax_1.safetensors)
[finetuned/classification_cvd/mnms_sax/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax/mnms_sax_2.safetensors)
[finetuned/classification_cvd/mnms_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax/config.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | +| CVD classification | M&Ms2 | SAX | 2 (ED and ES) | [finetuned/classification_cvd/mnms2_sax/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax/mnms2_sax_0.safetensors)
[finetuned/classification_cvd/mnms2_sax/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax/mnms2_sax_1.safetensors)
[finetuned/classification_cvd/mnms2_sax/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax/mnms2_sax_2.safetensors)
[finetuned/classification_cvd/mnms2_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax/config.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | +| CVD classification | M&Ms2 | LAX 4C | 2 (ED and ES) | [finetuned/classification_cvd/mnms2_lax_4c/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c/mnms2_lax_4c_0.safetensors)
[finetuned/classification_cvd/mnms2_lax_4c/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c/mnms2_lax_4c_1.safetensors)
[finetuned/classification_cvd/mnms2_lax_4c/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c/mnms2_lax_4c_2.safetensors)
[finetuned/classification_cvd/mnms2_lax_4c/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c/config.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | +| Patient sex classification | M&Ms | SAX | 2 (ED and ES) | [finetuned/classification_sex/mnms_sax/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax/mnms_sax_0.safetensors)
[finetuned/classification_sex/mnms_sax/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax/mnms_sax_1.safetensors)
[finetuned/classification_sex/mnms_sax/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax/mnms_sax_2.safetensors)
[finetuned/classification_sex/mnms_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax/config.yaml) | [classification_sex.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_sex.py) | +| CMR machine vendor classification | M&Ms2 | SAX | 2 (ED and ES) | [finetuned/classification_vendor/mnms2_sax/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax/mnms2_sax_0.safetensors)
[finetuned/classification_vendor/mnms2_sax/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax/mnms2_sax_1.safetensors)
[finetuned/classification_vendor/mnms2_sax/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax/mnms2_sax_2.safetensors)
[finetuned/classification_vendor/mnms2_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax/config.yaml) | [classification_vendor.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_vendor.py) | +| CMR machine vendor classification | M&Ms2 | LAX 4C | 2 (ED and ES) | [finetuned/classification_vendor/mnms2_lax_4c/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c/mnms2_lax_4c_0.safetensors)
[finetuned/classification_vendor/mnms2_lax_4c/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c/mnms2_lax_4c_1.safetensors)
[finetuned/classification_vendor/mnms2_lax_4c/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c/mnms2_lax_4c_2.safetensors)
[finetuned/classification_vendor/mnms2_lax_4c/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c/config.yaml) | [classification_vendor.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_vendor.py) | +| Direct EF regression | ACDC | SAX | 2 (ED and ES) | [finetuned/regression_ef/acdc_sax/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax/acdc_sax_0.safetensors)
[finetuned/regression_ef/acdc_sax/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax/acdc_sax_1.safetensors)
[finetuned/regression_ef/acdc_sax/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax/acdc_sax_2.safetensors)
[finetuned/regression_ef/acdc_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax/config.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | +| Direct EF regression | M&Ms | SAX | 2 (ED and ES) | [finetuned/regression_ef/mnms_sax/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax/mnms_sax_0.safetensors)
[finetuned/regression_ef/mnms_sax/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax/mnms_sax_1.safetensors)
[finetuned/regression_ef/mnms_sax/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax/mnms_sax_2.safetensors)
[finetuned/regression_ef/mnms_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax/config.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | +| Direct EF regression | M&Ms2 | SAX | 2 (ED and ES) | [finetuned/regression_ef/mnms2_sax/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax/mnms2_sax_0.safetensors)
[finetuned/regression_ef/mnms2_sax/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax/mnms2_sax_1.safetensors)
[finetuned/regression_ef/mnms2_sax/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax/mnms2_sax_2.safetensors)
[finetuned/regression_ef/mnms2_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax/config.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | +| Direct EF regression | M&Ms2 | LAX 4C | 2 (ED and ES) | [finetuned/regression_ef/mnms2_lax_4c/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c/mnms2_lax_4c_0.safetensors)
[finetuned/regression_ef/mnms2_lax_4c/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c/mnms2_lax_4c_1.safetensors)
[finetuned/regression_ef/mnms2_lax_4c/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c/mnms2_lax_4c_2.safetensors)
[finetuned/regression_ef/mnms2_lax_4c/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c/config.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | +| Patient BMI regression | ACDC | SAX | 2 (ED and ES) | [finetuned/regression_bmi/acdc_sax/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax/acdc_sax_0.safetensors)
[finetuned/regression_bmi/acdc_sax/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax/acdc_sax_1.safetensors)
[finetuned/regression_bmi/acdc_sax/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax/acdc_sax_2.safetensors)
[finetuned/regression_bmi/acdc_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax/config.yaml) | [regression_bmi.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_bmi.py) | +| Patient age regression | M&Ms | SAX | 2 (ED and ES) | [finetuned/regression_age/mnms_sax/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax/mnms_sax_0.safetensors)
[finetuned/regression_age/mnms_sax/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax/mnms_sax_1.safetensors)
[finetuned/regression_age/mnms_sax/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax/mnms_sax_2.safetensors)
[finetuned/regression_age/mnms_sax/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax/config.yaml) | [regression_age.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_age.py) | +| Landmark localization by heatmap regression | Landmark | LAX 2C | 1 | [finetuned/landmark_heatmap/lax_2c/lax_2c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c/lax_2c_0.safetensors)
[finetuned/landmark_heatmap/lax_2c/lax_2c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c/lax_2c_1.safetensors)
[finetuned/landmark_heatmap/lax_2c/lax_2c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c/lax_2c_2.safetensors)
[finetuned/landmark_heatmap/lax_2c/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c/config.yaml) | [landmark_heatmap.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_heatmap.py) | +| Landmark localization by heatmap regression | Landmark | LAX 4C | 1 | [finetuned/landmark_heatmap/lax_4c/lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c/lax_4c_0.safetensors)
[finetuned/landmark_heatmap/lax_4c/lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c/lax_4c_1.safetensors)
[finetuned/landmark_heatmap/lax_4c/lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c/lax_4c_2.safetensors)
[finetuned/landmark_heatmap/lax_4c/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c/config.yaml) | [landmark_heatmap.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_heatmap.py) | +| Landmark localization by coordinates regression | Landmark | LAX 2C | 1 | [finetuned/landmark_coordinate/lax_2c/lax_2c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c/lax_2c_0.safetensors)
[finetuned/landmark_coordinate/lax_2c/lax_2c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c/lax_2c_1.safetensors)
[finetuned/landmark_coordinate/lax_2c/lax_2c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c/lax_2c_2.safetensors)
[finetuned/landmark_coordinate/lax_2c/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c/config.yaml) | [landmark_coordinate.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_coordinate.py) | +| Landmark localization by coordinates regression | Landmark | LAX 4C | 1 | [finetuned/landmark_coordinate/lax_4c/lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c/lax_4c_0.safetensors)
[finetuned/landmark_coordinate/lax_4c/lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c/lax_4c_1.safetensors)
[finetuned/landmark_coordinate/lax_4c/lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c/lax_4c_2.safetensors)
[finetuned/landmark_coordinate/lax_4c/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c/config.yaml) | [landmark_coordinate.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_coordinate.py) | ## Pre-trained CineMA Model The pre-trained CineMA model backbone is available at [pretrained/cinema.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/pretrained/cinema.safetensors) with -configuration [pretrained/cinema.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/pretrained/cinema.yaml). +configuration [pretrained/config.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/pretrained/config.yaml). Following scripts demonstrated how to fine-tune this backbone using [a preprocessed version of ACDC dataset](https://huggingface.co/datasets/mathpluscode/ACDC): @@ -97,4 +77,4 @@ Following scripts demonstrated how to fine-tune this backbone using ## Contact -For questions or collaborations, please contact Yunguan Fu (yunguan.fu.18@ucl.ac.uk). \ No newline at end of file +For questions or collaborations, please contact Yunguan Fu (yunguan.fu.18@ucl.ac.uk). diff --git a/finetuned/classification_cvd/acdc_sax_0.safetensors b/finetuned/classification_cvd/acdc_sax/acdc_sax_0.safetensors similarity index 100% rename from finetuned/classification_cvd/acdc_sax_0.safetensors rename to finetuned/classification_cvd/acdc_sax/acdc_sax_0.safetensors diff --git a/finetuned/classification_cvd/acdc_sax_1.safetensors b/finetuned/classification_cvd/acdc_sax/acdc_sax_1.safetensors similarity index 100% rename from finetuned/classification_cvd/acdc_sax_1.safetensors rename to 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finetuned/segmentation/mnms2_lax_4c_1.safetensors rename to finetuned/segmentation/mnms2_lax_4c/mnms2_lax_4c_1.safetensors diff --git a/finetuned/segmentation/mnms2_lax_4c_2.safetensors b/finetuned/segmentation/mnms2_lax_4c/mnms2_lax_4c_2.safetensors similarity index 100% rename from finetuned/segmentation/mnms2_lax_4c_2.safetensors rename to finetuned/segmentation/mnms2_lax_4c/mnms2_lax_4c_2.safetensors diff --git a/finetuned/segmentation/mnms2_sax/config.yaml b/finetuned/segmentation/mnms2_sax/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..50684bc09883e9a102e3402854d0631395d6deab --- /dev/null +++ b/finetuned/segmentation/mnms2_sax/config.yaml @@ -0,0 +1,21 @@ +grad_ckpt: True +data: + sax: + spacing: [1.0, 1.0, 10.0] + patch_size: [192, 192, 16] + in_chans: 1 +model: + name: convunetr + views: sax + out_chans: 4 + convunetr: + size: base + enc_patch_size: [4, 4, 1] + enc_scale_factor: [2, 2, 1] + enc_conv_chans: [64, 128] + enc_conv_n_blocks: 2 + dec_chans: [32, 64, 128, 256, 512] + dec_patch_size: [2, 2, 1] + dec_scale_factor: [2, 2, 1] + dropout: 0.1 + drop_path: 0.1 diff --git a/finetuned/segmentation/mnms2_sax_0.safetensors b/finetuned/segmentation/mnms2_sax/mnms2_sax_0.safetensors similarity index 100% rename from finetuned/segmentation/mnms2_sax_0.safetensors rename to finetuned/segmentation/mnms2_sax/mnms2_sax_0.safetensors diff --git a/finetuned/segmentation/mnms2_sax_1.safetensors b/finetuned/segmentation/mnms2_sax/mnms2_sax_1.safetensors similarity index 100% rename from finetuned/segmentation/mnms2_sax_1.safetensors rename to finetuned/segmentation/mnms2_sax/mnms2_sax_1.safetensors diff --git a/finetuned/segmentation/mnms2_sax_2.safetensors b/finetuned/segmentation/mnms2_sax/mnms2_sax_2.safetensors similarity index 100% rename from finetuned/segmentation/mnms2_sax_2.safetensors rename to finetuned/segmentation/mnms2_sax/mnms2_sax_2.safetensors diff --git a/finetuned/segmentation/mnms_sax/config.yaml b/finetuned/segmentation/mnms_sax/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..50684bc09883e9a102e3402854d0631395d6deab --- /dev/null +++ b/finetuned/segmentation/mnms_sax/config.yaml @@ -0,0 +1,21 @@ +grad_ckpt: True +data: + sax: + spacing: [1.0, 1.0, 10.0] + patch_size: [192, 192, 16] + in_chans: 1 +model: + name: convunetr + views: sax + out_chans: 4 + convunetr: + size: base + enc_patch_size: [4, 4, 1] + enc_scale_factor: [2, 2, 1] + enc_conv_chans: [64, 128] + enc_conv_n_blocks: 2 + dec_chans: [32, 64, 128, 256, 512] + dec_patch_size: [2, 2, 1] + dec_scale_factor: [2, 2, 1] + dropout: 0.1 + drop_path: 0.1 diff --git a/finetuned/segmentation/mnms_sax_0.safetensors b/finetuned/segmentation/mnms_sax/mnms_sax_0.safetensors similarity index 100% rename from finetuned/segmentation/mnms_sax_0.safetensors rename to finetuned/segmentation/mnms_sax/mnms_sax_0.safetensors diff --git a/finetuned/segmentation/mnms_sax_1.safetensors b/finetuned/segmentation/mnms_sax/mnms_sax_1.safetensors similarity index 100% rename from finetuned/segmentation/mnms_sax_1.safetensors rename to finetuned/segmentation/mnms_sax/mnms_sax_1.safetensors diff --git a/finetuned/segmentation/mnms_sax_2.safetensors b/finetuned/segmentation/mnms_sax/mnms_sax_2.safetensors similarity index 100% rename from finetuned/segmentation/mnms_sax_2.safetensors rename to finetuned/segmentation/mnms_sax/mnms_sax_2.safetensors diff --git a/pretrained/cinema.yaml b/pretrained/config.yaml similarity index 100% rename from pretrained/cinema.yaml rename to pretrained/config.yaml