data set preprocessing

[huyue132]

Hello, I would like to try other parts segmentation. Is there any public data preprocessing script? Can you share it? Thank you

[peterant330]

Hi,

The major part of the data preprocessing is included in the dataloader. Please refer to 3DSAM-adapter/dataset/base_dataset.py and 3DSAM-adapter/dataset/datasets.py. The input to the dataloader is actually the original nii.gz file without preprocessing. The only process is to arrange the files into a folder.

While you may need to calculate the intensity_range, global_mean and global_std, they are calculated as the 99.5 and 0.5 percentile, mean and std of the foreground pixels across the training data. You may also use other values such as the windows provided by the clinicians.

[csp2002]

I noticed that you provided the preprocessed dataset download link. After downloading it, I found that it includes nii.gz files and a split.pkl file. Are those nii.gz files the same as the original data downloaded from the official challenge? In other words, if I have downloaded the nii.gz files from the official challenge website, the only thing I need is the split.pkl, is it right? Thanks!

[peterant330]

I noticed that you provided the preprocessed dataset download link. After downloading it, I found that it includes nii.gz files and a split.pkl file. Are those nii.gz files the same as the original data downloaded from the official challenge? In other words, if I have downloaded the nii.gz files from the official challenge website, the only thing I need is the split.pkl, is it right? Thanks!

Yes, you are right.

[zzzyzh]

Thanks for the author's patience in replying
How can I generate a suitable split.pkl file for my dataset?