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ViT UNETR SSL #10

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ViT UNETR SSL #10

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Commits on Mar 8, 2024

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  2. Fix typo

    valosekj committed Mar 8, 2024
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  4. Fix typo

    valosekj committed Mar 8, 2024
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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
    valosekj committed Mar 8, 2024
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Commits on Mar 9, 2024

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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 committed Mar 9, 2024
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  4. update description

    valosekj committed Mar 9, 2024
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  9. remove 'to_onehot_y=True' and 'softmax=True' because we work with sin…

    …gle channel prediction
    valosekj committed Mar 9, 2024
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Commits on Mar 12, 2024

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  3. Add 'keys' arg

    valosekj committed Mar 12, 2024
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  4. Add 'keys' arg

    valosekj committed Mar 12, 2024
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  6. Update comments

    valosekj committed Mar 12, 2024
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  7. Fix imports

    valosekj committed Mar 12, 2024
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  9. Make '--data' non required

    valosekj committed Mar 12, 2024
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Commits on Mar 13, 2024

  1. Update input arg description

    valosekj committed Mar 13, 2024
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  2. Rerun the notebook

    valosekj committed Mar 13, 2024
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  4. Add '--cuda' input arg

    valosekj committed Mar 13, 2024
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Commits on Mar 15, 2024

  1. track and save epoch time

    valosekj committed Mar 15, 2024
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  3. Add comment

    valosekj committed Mar 15, 2024
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  6. Add 'torch.multiprocessing.set_sharing_strategy('file_system')' to so…

    …lve number of workers issue
    
    Fixes: #8
    valosekj committed Mar 15, 2024
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  9. Link issue

    valosekj committed Mar 15, 2024
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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)
    valosekj committed Mar 15, 2024
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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
    valosekj committed Mar 15, 2024
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Commits on Mar 16, 2024

  1. typo

    valosekj committed Mar 16, 2024
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  2. batch_size = 8

    valosekj committed Mar 16, 2024
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  3. NUM_WORKERS = batch_size

    valosekj committed Mar 16, 2024
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  4. number_of_holes=5

    number of holes to be used for the RandCoarseDropoutd and RandCoarseShuffled transforms
    valosekj committed Mar 16, 2024
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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 and naga-karthik authored Mar 16, 2024
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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 committed Mar 17, 2024
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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
    valosekj committed Mar 17, 2024
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Commits on Mar 18, 2024

  1. Add '--cuda' input arg

    valosekj committed Mar 18, 2024
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  2. Remove 'AsDiscrete'

    valosekj committed Mar 18, 2024
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  3. Remove 'AsDiscrete'

    valosekj committed Mar 18, 2024
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  4. Add 'CUDA_NUM=args.cuda'

    valosekj committed Mar 18, 2024
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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)
    valosekj committed Mar 18, 2024
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  8. batch_size = 8

    valosekj committed Mar 18, 2024
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  9. NUM_WORKERS = batch_size

    valosekj committed Mar 18, 2024
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  11. Fix shape logging

    valosekj committed Mar 18, 2024
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  17. update docstring

    valosekj committed Mar 18, 2024
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Commits on Mar 19, 2024

  1. Plot GT together with image

    valosekj committed Mar 19, 2024
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  3. update output fig fname

    valosekj committed Mar 19, 2024
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  5. threshold val_labels_list and val_outputs_list by 0.5 threshold befor…

    …e computing validation dice and plotting
    valosekj committed Mar 19, 2024
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  7. fix binarization bug

    naga-karthik committed Mar 19, 2024
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Commits on Mar 20, 2024

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  2. Add debug lines

    valosekj committed Mar 20, 2024
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  3. PEP8

    valosekj committed Mar 20, 2024
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  5. improve comments

    valosekj committed Mar 20, 2024
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  6. fix figure title

    valosekj committed Mar 20, 2024
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Commits on Mar 21, 2024

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Commits on Mar 22, 2024

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  2. run notebook again

    valosekj committed Mar 22, 2024
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Commits on Mar 23, 2024

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Commits on Mar 24, 2024

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  2. fix typo

    valosekj committed Mar 24, 2024
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  3. remove unused imports

    valosekj committed Mar 24, 2024
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  4. fix sc suffix for sci-paris

    valosekj committed Mar 24, 2024
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  6. Update logging message

    valosekj committed Mar 24, 2024
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