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image-segmentationnifti

Loading nii.zip (compressed) 3d segmentation files

I know SimpleITK can read 3d images in Nifty (.nii) format, and also that it supports nii.gz compressed version. However, I am not able to load nii.zip files. These files throw error if I try to unzip/extract them directly, and also not recognized as one of the readable formats by SimpleITK.

Dataset for reference can be found in: https://academictorrents.com/details/27772adef6f563a1ecc0ae19a528b956e6c803ce

Solution

  • I downloaded the same dataset a while ago, I did not experiment with it thoroughly, but here is my experience:

    1. I am able to unzip the nii.zip files succesfully

      • I am using Linux Ubuntu 18.04 and preinstalled unzipping utility from GUI
      • The problems you are experiencing could be happening due to using different archive manager or maybe the dataset could have been damaged during download
      • solution - try different archive manager and download the dataset again

    2. I am using Aliza to view the unzipped scans

      • from my experience for quick checking of the medical image formats Aliza viewer is the best program available with possible exports to different formats

    3. Solution for reading zipped files