ViT UNETR SSL #10

valosekj · 2024-03-16T14:28:47Z

Just a draft PR to allow commit suggestions

…(ViT)

- `patch_size=(16, 16, 16)` - to fix tensor size mismatch - `batch_size = 2` - to handle memory

…ned model

…ation Model Using SSL Pre-trained Weights

…gle channel prediction

…ches

…of ancdata'

…e computing validation dice and plotting

…atch

…ple datasets

valosekj added 30 commits March 8, 2024 10:17

Add notebook debugging SSL pretraining transformations

75a5f85

Fix typo

e37ff59

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

80fd7db

…(ViT)

Fix typo

4dc7e81

Do sanity dimension check after transformations

3a9baef

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

4517f7a

- `patch_size=(16, 16, 16)` - to fix tensor size mismatch - `batch_size = 2` - to handle memory

rename 'crop_size' to 'spatial_size'

a621a9a

use 'contrast-agnostic' data augmentation for Training of the fine-tu…

516f1ec

…ned model

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

fd8f943

…ation Model Using SSL Pre-trained Weights

update description

d1b9c3d

use 'logger.info' instead of 'print'

45ef357

make '--data' arg notrequired

0955689

explicitly specify CUDA GPU number

9ea8bca

change sliding_window_inference roi_size and batch_size

3bc999a

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

8e8a977

…gle channel prediction

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

42394e8

…ches

rerun the notebook to show different slices

622c3f6

Add 'keys' arg

59f4db0

Add 'keys' arg

a3ae050

Update 'RandCoarseDropoutd' params

e1cfad1

Update comments

d4e9995

Fix imports

4c35d42

Change batch_size and NUM_WORKERS to 4

05ab59a

Make '--data' non required

0b12c10

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

f5881aa

…of ancdata'

Update input arg description

7aa9858

Rerun the notebook

16691d7

Print hyper-parameters into the log file

56ca187

Add '--cuda' input arg

ce7315a

track and save epoch time

1ebf833

valosekj and others added 30 commits March 18, 2024 19:34

Save validation figure only if it contains a lesion

f34ece1

Plot GT together with image

e0afafe

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

e588a22

update output fig fname

2d0b530

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

988680e

threshold val_labels_list and val_outputs_list by 0.5 threshold befor…

f675611

…e computing validation dice and plotting

add normalized relu normalization

cc78896

fix binarization bug

92334ea

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

2c49ca2

overlay prediction over input image

fbe3dd7

Fix variable when getting probabilities from logits

ba39d28

Add debug lines

c8d9a5d

PEP8

ac040a5

Set validation batch_size to 1

1e2b61d

improve comments

8f49545

fix figure title

3a74e28

comment 'AsDiscreted' transforms

dea121c

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

013ca65

…atch

Add script to create spine-generic MSD dataset

f1aae1b

run notebook again

e4c87be

Make 'create_msd_data.py' compatible with other BIDS datasets

4448356

Add note that no testing set is created

a354a21

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

141c96b

…ple datasets

fix typo

7f8e6bb

remove unused imports

46f1bd9

fix sc suffix for sci-paris

afeb7c5

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

da1c131

Update logging message

ed42c68

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

7f28fed

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

99a936b

Provide feedback

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ViT UNETR SSL #10

ViT UNETR SSL #10

valosekj commented Mar 16, 2024

ViT UNETR SSL #10

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ViT UNETR SSL #10

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valosekj commented Mar 16, 2024