Link to dataset

[moeinheidari7829]

Hi there,

Thank you so much for open-sourcing your amazing work. I was wondering if it would be possible for you to share a link to one of the datasets used in the paper (such as BRATS) formatted in the same way that your dataloader reads the data? I would greatly appreciate it.

Thank you in advance!

[bilalkabas]

Hi,

Thank you for your interest in our research. We released a dataset preparation script for BraTS (2021) dataset. This script can be modified for other datasets as well. It takes the original dataset and creates the one that our dataloader expects.

Following links can be used to download original datasets:

• IXI
• BraTS (2015)
• BraTS (2021)

[moeinheidari7829]

Hi,

Thank you for your interest in our research. We released a dataset preparation script for BraTS (2021) dataset. This script can be modified for other datasets as well. It takes the original dataset and creates the one that our dataloader expects.

Following links can be used to download original datasets:

• IXI
• BraTS (2015)
• BraTS (2021)

Hi, thank you for responding to my questions and for sharing the code to organize the data. I have downloaded and preprocessed the data as outlined in the repository and trained the model using the same configurations as yours.
However, I am encountering inconsistent and poor results, as shown in the attached image, along with NaN values for PSNR and SSIM. Have you experienced a similar issue? I am running the code without any modifications to reproduce the result

epoch_49

[bilalkabas]

Hi,

We performed our experiments using BraTS 2015 dataset. I have shared a link to the BraTS 2021 along with the preprocessing script as it is easier to access and start experimentation straightaway. After performing debugging, I have detected 2 issues with the preprocessing script that I shared with you: (1) an overwrite issue causing each split to only have a single volume (a total of 155 slices), (2) empty slices at the beginning and end of the volumes. These are the reasons for the poor performance and NaN values.

I have updated the preprocessing script accordingly. Now, it expects the directory where you unzipped the original BraTS 2021 dataset. It creates train, val, test splits and then the formatted dataset.

Please not that this will not reproduce the exact results in the paper as it is the 2021 version. However, it is going to produce valid and similar results.

Thank you for your time.