Figures added, pretrained weights link added, minor fixes (#456)

* Figures added, pretrained weights link added, minor fixes

Signed-off-by: vnath <vnath@nvidia.com>

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Co-authored-by: vnath <vnath@nvidia.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: finalelement

figures/SSL_Different_Augviews.png

@@ -1,34 +1,42 @@
-# Self-Supervised Pretraining Tutorial
+# Self-Supervised Pre-training Tutorial
 
 This directory contains two scripts. The first script 'ssl_script_train.py' generates
 a good set of pre-trained weights using unlabeled data with self-supervised tasks that
 are based on augmentations of different types. The second script 'ssl_finetune_train.py' uses
 the pre-trained weights generated from the first script and performs fine-tuning on a fully supervised
 task.
 
+In case, the user wants to skip the pre-training part, the pre-trained weights can be
+[downloaded from here](https://drive.google.com/file/d/1z0BouIiQ9oLizubOIH9Rlpad5Kk_2RtY/view?usp=sharing)
+to use for fine-tuning tasks and directly skip to the second part of the tutorial which is using the
+'ssl_finetune_train.py'.
+
 ### Steps to run the tutorial
 1.) Download the two datasets [TCIA-Covid19](https://wiki.cancerimagingarchive.net/display/Public/CT+Images+in+COVID-19)
 & [BTCV](https://www.synapse.org/#!Synapse:syn3193805/wiki/217789) (More detail about them in the Data section)\
 2.) Modify the paths for data_root, json_path & logdir in ssl_script_train.py\
 3.) Run the 'ssl_script_train.py'\
-4.) Modify the paths for data_root, json_path, pretrained_weights_path from 2.) and
+4.) Modify the paths for data_root, json_path, pre-trained_weights_path from 2.) and
 logdir_path in 'ssl_finetuning_train.py'\
 5.) Run the ssl_finetuning_script.py\
 6.) And that's all folks, use the model to your needs
 
 ### 1.Data
-Pretraining Dataset: The TCIA Covid-19 dataset was used for generating the pretrained weights.
+Pre-training Dataset: The TCIA Covid-19 dataset was used for generating the
+[pre-trained weights](https://drive.google.com/file/d/1z0BouIiQ9oLizubOIH9Rlpad5Kk_2RtY/view?usp=sharing).
 The dataset contains a total of 771 3D CT Volumes. The volumes were split into training and validation sets
-of 600 and 171 3D volumes correspondingly. The data is available for download at this [link](https://wiki.cancerimagingarchive.net/display/Public/CT+Images+in+COVID-19).
-If this dataset is being used in your work
-please use [1] as reference. A json file is provided which contains the suggested training and validation split
-in the json_files directory of the self-supervised training tutorial.
-
-Fine-tuning Dataset: The dataset from Beyond the Cranial Vault Challenge [(BTCV)](https://www.synapse.org/#!Synapse:syn3193805/wiki/217789)
-2015 hosted at MICCAI was used as a fully supervised fine-tuning task on the pre-trained weights. The dataset
-consists of 30 3D Volumes with annotated labels of upto 13 different organs [2]. There are 3 json files provided in the
-json_files directory for the dataset. They correspond to having different number of training volumes ranging 6, 12 and 24.
-All 3 json files have the same validation split.
+of 600 and 171 3D volumes correspondingly. The data is available for download at this
+[link](https://wiki.cancerimagingarchive.net/display/Public/CT+Images+in+COVID-19).
+If this dataset is being used in your work,  please use [1] as reference. A json file is provided
+which contains the training and validation splits that were used for the training. The json file can be found in the
+json_files directory of the self-supervised training tutorial.
+
+Fine-tuning Dataset: The dataset from Beyond the Cranial Vault Challenge
+[(BTCV)](https://www.synapse.org/#!Synapse:syn3193805/wiki/217789)
+2015 hosted at MICCAI, was used as a fully supervised fine-tuning task on the pre-trained weights. The dataset
+consists of 30 3D Volumes with annotated labels of up to 13 different organs [2]. There are 3 json files provided in the
+json_files directory for the dataset. They correspond to having different number of training volumes ranging from
+6, 12 and 24. All 3 json files have the same validation split.
 
 References:
 
@@ -40,14 +48,15 @@ Medical Image Analysis 69 (2021): 101894.
 
 ### 2. Network Architectures
 
-For pretraining a modified version of ViT [1] has been used, it can be referred [here](https://docs.monai.io/en/latest/networks.html#vitautoenc)
+For pre-training a modified version of ViT [1] has been used, it can be referred
+[here](https://docs.monai.io/en/latest/networks.html#vitautoenc)
 from MONAI. The original ViT was modified by attachment of two 3D Convolutional Transpose Layers to achieve a similar
-reconstruction size as that of the input image. The ViT is the backbone for the UNETR [2] network architecture which was
-used for the fine-tuning fully supervised tasks.
+reconstruction size as that of the input image. The ViT is the backbone for the UNETR [2] network architecture which
+was used for the fine-tuning fully supervised tasks.
 
-The pretrained backbone of ViT weights were loaded to UNETR and the decoder head still relies on random initialization
+The pre-trained backbone of ViT weights were loaded to UNETR and the decoder head still relies on random initialization
 for adaptability of the new downstream task. This flexibility also allows the user to adapt the ViT backbone to their
-own custom created network architectures as well which uses the ViT backbone.
+own custom created network architectures as well.
 
 References:
 
@@ -59,29 +68,33 @@ arXiv preprint arXiv:2103.10504 (2021).
 
 ### 3. Self-supervised Tasks
 
-The pretraining pipeline has two aspects to it. The first it uses augmentation to mutate the data and the second is
-it utilizes to a regularized [constrastive loss](https://docs.monai.io/en/latest/losses.html#contrastiveloss) [3] to
-learn feature representations of the unlabeled data. The multiple augmentations are applied on a randomly selected 3D
-foreground patch from a 3D volume. Two augmented views of the same 3D patch are generated for the constrastive loss as
-it functions by drawing the two augmented views closer to each other.
+The pre-training pipeline has two aspects to it (Refer figure shown below). First, it uses augmentation (top row) to
+mutate the data and the second is it utilizes to a regularized
+[constrastive loss](https://docs.monai.io/en/latest/losses.html#contrastiveloss) [3] to learn feature representations
+of the unlabeled data. The multiple augmentations are applied on a randomly selected 3D foreground patch from a 3D
+volume. Two augmented views of the same 3D patch are generated for the contrastive loss as it functions by drawing
+the two augmented views closer to each other if the views are generated from the same patch, if not then it tries to
+maximize the disagreement. The CL offers this functionality on a mini-batch.
+
+![image](../figures/SSL_Overview_Figure.png)
 
-The augmentations mutate the 3D patch in different ways and the primary task of the network is to reconstruct
+The augmentations mutate the 3D patch in various ways, the primary task of the network is to reconstruct
 the original image. The different augmentations used are classical techniques such as in-painting [1], out-painting [1]
 and noise augmentation to the image by local pixel shuffling [2]. The secondary task of the network is to simultaneously
-reconstruct the two augmented views as similar to each other as possible via the regularized contrastive loss [3] as it's
-objective is to maximize the agreement. The term regularized has been used here because the contrastive loss is adjusted
+reconstruct the two augmented views as similar to each other as possible via regularized contrastive loss [3] as it's
+objective is to maximize the agreement. The term regularized has been used here because contrastive loss is adjusted
 by the reconstruction loss as a dynamic weight itself.
 
-The below example image depicts the usage of the augmentations pipeline where two augmented views are drawn of the same
+The below example image depicts the usage of the augmentation pipeline where two augmented views are drawn of the same
 3D patch:
 
-![image](../figures/ssl_aug_views.png)
+![image](../figures/SSL_Different_Augviews.png)
 
-The three columns are the three views of axial, coronal, sagittal of a randomly selected patch of size 96x96x96.
-The top row is the ground truth image which is not augmented. The middle row is the same image when mutated by augmentations.
-The bottom row is a 2nd view of the same patch but augmented with different probabilities
-The objective of the SSL network is to reconstruct the original top row image from the first view. The contrastive loss
-is driven by maximizing agreement of the reconstruction based on input of the two augmented views .
+Multiple axial slice of a 96x96x96 patch are shown before the augmentation (Ref Original Patch in the above figure).
+Augmented View 1 & 2 are different augmentations generated via the transforms on the same cubic patch. The objective
+of the SSL network is to reconstruct the original top row image from the first view. The contrastive loss
+is driven by maximizing agreement of the reconstruction based on input of the two augmented views.
+`matshow3d` from `monai.visualize` was used for creating this figure, a tutorial for using can be found [here](https://github.com/Project-MONAI/tutorials/blob/master/modules/transform_visualization.ipynb)
 
 References:
 
@@ -104,23 +117,25 @@ Batch size: 4 3D Volumes (Total of 8 as 2 samples were drawn per 3D Volume) \
 Loss Function: L1
 Contrastive Loss Temperature: 0.005
 
-Training Hyper-parameters for Fine-tuning BTCV task (All settings have been kept consistent with prior [UNETR 3D
+Training Hyper-parameters for Fine-tuning BTCV task (All settings have been kept consistent with prior
+[UNETR 3D
 Segmentation tutorial](https://github.com/Project-MONAI/tutorials/blob/master/3d_segmentation/unetr_btcv_segmentation_3d.ipynb)): \
 Number of Steps: 30000 \
 Validation Frequency: 100 steps \
 Batch Size: 1 3D Volume (4 samples are drawn per 3D volume) \
 Learning Rate: 1e-4 \
 Loss Function: DiceCELoss
 
-### 4. Training & Validation Curves for pretraining SSL
+### 4. Training & Validation Curves for pre-training SSL
 
 ![image](../figures/ssl_pretrain_losses.png)
 
-L1 error reported for training and validation when performing the SSL training
+L1 error reported for training and validation when performing the SSL training. Please note contrastive loss is not
+L1.
 
 ### 5. Results of the Fine-tuning vs Random Initialization on BTCV
 
-| Training Volumes      | Validation Volumes | Random Init Dice score | Pretrained Dice Score | Relative Performance Improvement |
+| Training Volumes      | Validation Volumes | Random Init Dice score | Pre-trained Dice Score | Relative Performance Improvement |
 | ----------------      | ----------------   | ----------------       | ----------------      | ----------------        |
 | 6      | 6 | 63.07 | 70.09 | ~11.13% |
 | 12      | 6 | 76.06 | 79.55 | ~4.58% |