Extract/Save ROI from seg.nrrd (segmentations file) using Python packages SimpleITK or Slicerio

Vishal_P
Wed, 13 Dec 2023 00:40:48 +0000
Support

Hello!

I have a .nii scan file and have successfully created segments, saving them in a .seg.nrrd file. My goal now is to extract ROIs based on label names and save them as new .nii files. To achieve this, I am exploring the use of SimpleITK and the SlicerIO package.

i want to perform the multiplication between an ROI mask (based on Label Name) and the original scan file, resulting in an extracted ROI region. without broadcast error or shape mismatch error.

and does the seg.nrrd file contain the voxels from scan file for each ROI or just ROI masks?

Thank You!

5 posts - 3 participants