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ViT UNETR SSL #10

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Commits on Mar 8, 2024

  1. Add notebook debugging SSL pretraining transformations

    @valosekj
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  2. Fix typo

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  3. Add script for Self-Supervised Pre-training using Vision Transformer … 

    …(ViT)
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  4. Fix typo

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  5. Do sanity dimension check after transformations

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  6. Use patch_size=(16, 16, 16) and batch_size = 2 

    - `patch_size=(16, 16, 16)` - to fix tensor size mismatch
- `batch_size = 2` - to handle memory
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Commits on Mar 9, 2024

  1. rename 'crop_size' to 'spatial_size'

    @valosekj
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  2. use 'contrast-agnostic' data augmentation for Training of the fine-tu… 

    …ned model
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  3. Add script to finetune the 3D Single-Class Spinal Cord Lesion Segment… 

    …ation Model Using SSL Pre-trained Weights
    @valosekj
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  4. update description

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  5. use 'logger.info' instead of 'print'

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  6. make '--data' arg notrequired

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  7. explicitly specify CUDA GPU number

    @valosekj
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  8. change sliding_window_inference roi_size and batch_size

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  9. remove 'to_onehot_y=True' and 'softmax=True' because we work with sin… 

    …gle channel prediction
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Commits on Mar 12, 2024

  1. add notebook to debug transformations when using SC masks to crop pat… 

    …ches
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  2. rerun the notebook to show different slices

    @valosekj
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  3. Add 'keys' arg

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  4. Add 'keys' arg

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  5. Update 'RandCoarseDropoutd' params

    @valosekj
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  6. Update comments

    @valosekj
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  7. Fix imports

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  8. Change batch_size and NUM_WORKERS to 4

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  9. Make '--data' non required

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  10. change 'num_workers' to 0 to prevent 'RuntimeError: received 0 items … 

    …of ancdata'
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Commits on Mar 13, 2024

  1. Update input arg description

    @valosekj
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  2. Rerun the notebook

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  3. Print hyper-parameters into the log file

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  4. Add '--cuda' input arg

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Commits on Mar 15, 2024

  1. track and save epoch time

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  2. Plot and save input and output validation images to see how the model… 

    … is learning
    @valosekj
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  3. Add comment

    @valosekj
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  4. Do not plot 'outputs_v2' as it is a hidden representation

    @valosekj
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  5. Include the epoch number as master title

    @valosekj
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  6. Add 'torch.multiprocessing.set_sharing_strategy('file_system')' to so… 

    …lve number of workers issue

Fixes: #8
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  7. Create validation_figures directory if it does not exist

    @valosekj
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  8. Use 3 leading zeros for the epoch number in the figures fname

    @valosekj
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  9. Link issue

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  10. Add note for 'RandCropByPosNegLabeld' 

    It seems that the transform randomly selects a foreground point from image, then use it as center crop. This means that it can find the closest voxel that is just outside the SC and use it as the center (hence it includes the SC).
Source: Project-MONAI/MONAI#452 (comment)
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  11. Add 'number_of_holes' arg to specify the number of holes to be used f… 

    …or the RandCoarseDropoutd and RandCoarseShuffled transforms
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Commits on Mar 16, 2024

  1. typo

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  2. batch_size = 8

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  3. NUM_WORKERS = batch_size

    @valosekj
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  4. number_of_holes=5 

    number of holes to be used for the RandCoarseDropoutd and RandCoarseShuffled transforms
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  5. Update transforms for training of the fine-tuned model 

    From contrast-agnostic SC seg transforms (which heavily deform the image) to simpler transforms more suitable for lesion seg.
Context: #10 (comment)

Co-authored-by: Naga Karthik Enamundram <[email protected]>
    @valosekj @naga-karthik
    valosekj and naga-karthik authored Mar 16, 2024
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  6. update comment, remove unused imports

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  7. Add notebook with RandCoarseDropoutd transform debug

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Commits on Mar 17, 2024

  1. Fix 'dropout_holes=True' and 'dropout_holes=False' comments 

    From MONAI doc (https://docs.monai.io/en/latest/transforms.html#randcoarsedropoutd):
- if True, dropout the regions of holes and fill value specified by 'fill_value'
- if False, keep the holes and dropout the outside and fill value specified by 'fill_value'
    @valosekj
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  2. remove unused 'max_spatial_size' arg

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  3. use 'fill_value=0' for 'RandCoarseDropoutd'

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  4. Plot also RandCoarseDropoutd dropout_holes=False fill_value=0

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  5. Add note that the batch size is actually doubled (8*2=16), because we… 

    … are using two augmented samples per 3D Volume
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Commits on Mar 18, 2024

  1. Add '--cuda' input arg

    @valosekj
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  2. Remove 'AsDiscrete'

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  3. Remove 'AsDiscrete'

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  4. Add 'CUDA_NUM=args.cuda'

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  5. Add TODO to increase batch_size to 16

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  6. Use 'roi_size' for 'define_finetune_train_transforms'

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  7. Use 'label_sc' to crop samples around the SC 

    - we have to do  it because the pretrained model was trained on samples of (64, 64, 64)
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  8. batch_size = 8

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  9. NUM_WORKERS = batch_size

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  10. Add 'import torch.multiprocessing'

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  11. Fix shape logging

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  12. Change 'img_size' to 'ROI_SIZE'

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  13. 'batch["label"]' --> 'batch["label_lesion"]'

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  14. Plot and save input and output validation images to see how the model… 

    … is learning
    @valosekj
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  15. Fix ROI_SIZE for sliding_window_inference

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  16. Crop samples of 64x64x64 also for Validation of the fine-tuned model

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  17. update docstring

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  18. log validation samples shapes

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  19. Save validation figure only if it contains a lesion

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Commits on Mar 19, 2024

  1. Plot GT together with image

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  2. print unique values in the slice to see if it is binary

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  3. update output fig fname

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  4. Add 'AsDiscreted' for Training and Validation of the fine-tuned model

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  5. threshold val_labels_list and val_outputs_list by 0.5 threshold befor… 

    …e computing validation dice and plotting
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  6. add normalized relu normalization

    @naga-karthik
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  7. fix binarization bug

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  8. remove 'logger.info(np.unique(output.detach().cpu().numpy()))'

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  9. overlay prediction over input image

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Commits on Mar 20, 2024

  1. Fix variable when getting probabilities from logits

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  2. Add debug lines

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  3. PEP8

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  4. Set validation batch_size to 1

    @valosekj
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  5. improve comments

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  6. fix figure title

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  7. comment 'AsDiscreted' transforms

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Commits on Mar 21, 2024

  1. Make '--pretrained-model' non required to allow training from the scr… 

    …atch
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Commits on Mar 22, 2024

  1. Add script to create spine-generic MSD dataset

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  2. run notebook again

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Commits on Mar 23, 2024

  1. Make 'create_msd_data.py' compatible with other BIDS datasets

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  2. Add note that no testing set is created

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Commits on Mar 24, 2024

  1. Add README with instructions on how to download T2w images from multi… 

    …ple datasets
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  2. fix typo

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  3. remove unused imports

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  4. fix sc suffix for sci-paris

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  5. Use os.path.abspath for 'args.path_data' and 'args.path_out'

    @valosekj
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  6. Update logging message

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  7. Fix '.replace' to prevent '//' in the output string

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  8. Add 'create_msd_data.py' commands to create MSD-style JSON datalists

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