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ViT UNETR SSL #10

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Just a draft PR to allow commit suggestions

valosekj added 30 commits March 8, 2024 10:17
@valosekj
Add notebook debugging SSL pretraining transformations
75a5f85
@valosekj
Fix typo
e37ff59
@valosekj
Add script for Self-Supervised Pre-training using Vision Transformer …
80fd7db 
…(ViT)
@valosekj
Fix typo
4dc7e81
@valosekj
Do sanity dimension check after transformations
3a9baef
@valosekj
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
@valosekj
rename 'crop_size' to 'spatial_size'
a621a9a
@valosekj
use 'contrast-agnostic' data augmentation for Training of the fine-tu…
516f1ec 
…ned model
@valosekj
Add script to finetune the 3D Single-Class Spinal Cord Lesion Segment…
fd8f943 
…ation Model Using SSL Pre-trained Weights
@valosekj
update description
d1b9c3d
@valosekj
use 'logger.info' instead of 'print'
45ef357
@valosekj
make '--data' arg notrequired
0955689
@valosekj
explicitly specify CUDA GPU number
9ea8bca
@valosekj
change sliding_window_inference roi_size and batch_size
3bc999a
@valosekj
remove 'to_onehot_y=True' and 'softmax=True' because we work with sin…
8e8a977 
…gle channel prediction
@valosekj
add notebook to debug transformations when using SC masks to crop pat…
42394e8 
…ches
@valosekj
rerun the notebook to show different slices
622c3f6
@valosekj
Add 'keys' arg
59f4db0
@valosekj
Add 'keys' arg
a3ae050
@valosekj
Update 'RandCoarseDropoutd' params
e1cfad1
@valosekj
Update comments
d4e9995
@valosekj
Fix imports
4c35d42
@valosekj
Change batch_size and NUM_WORKERS to 4
05ab59a
@valosekj
Make '--data' non required
0b12c10
@valosekj
change 'num_workers' to 0 to prevent 'RuntimeError: received 0 items …
f5881aa 
…of ancdata'
@valosekj
Update input arg description
7aa9858
@valosekj
Rerun the notebook
16691d7
@valosekj
Print hyper-parameters into the log file
56ca187
@valosekj
Add '--cuda' input arg
ce7315a
@valosekj
track and save epoch time
1ebf833
valosekj and others added 30 commits March 18, 2024 19:34
@valosekj
Save validation figure only if it contains a lesion
f34ece1
@valosekj
Plot GT together with image
e0afafe
@valosekj
print unique values in the slice to see if it is binary
e588a22
@valosekj
update output fig fname
2d0b530
@valosekj
Add 'AsDiscreted' for Training and Validation of the fine-tuned model
988680e
@valosekj
threshold val_labels_list and val_outputs_list by 0.5 threshold befor…
f675611 
…e computing validation dice and plotting
@naga-karthik
add normalized relu normalization
cc78896
@naga-karthik
fix binarization bug
92334ea
@valosekj
remove 'logger.info(np.unique(output.detach().cpu().numpy()))'
2c49ca2
@valosekj
overlay prediction over input image
fbe3dd7
@valosekj
Fix variable when getting probabilities from logits
ba39d28
@valosekj
Add debug lines
c8d9a5d
@valosekj
PEP8
ac040a5
@valosekj
Set validation batch_size to 1
1e2b61d
@valosekj
improve comments
8f49545
@valosekj
fix figure title
3a74e28
@valosekj
comment 'AsDiscreted' transforms
dea121c
@valosekj
Make '--pretrained-model' non required to allow training from the scr…
013ca65 
…atch
@valosekj
Add script to create spine-generic MSD dataset
f1aae1b
@valosekj
run notebook again
e4c87be
@valosekj
Make 'create_msd_data.py' compatible with other BIDS datasets
4448356
@valosekj
Add note that no testing set is created
a354a21
@valosekj
Add README with instructions on how to download T2w images from multi…
141c96b 
…ple datasets
@valosekj
fix typo
7f8e6bb
@valosekj
remove unused imports
46f1bd9
@valosekj
fix sc suffix for sci-paris
afeb7c5
@valosekj
Use os.path.abspath for 'args.path_data' and 'args.path_out'
da1c131
@valosekj
Update logging message
ed42c68
@valosekj
Fix '.replace' to prevent '//' in the output string
7f28fed
@valosekj
Add 'create_msd_data.py' commands to create MSD-style JSON datalists
99a936b
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@valosekj @naga-karthik