How to process only few slices of a 3D dicom image

#1

Hi All,

I have a use case where given a 3D dicom image, I wish to apply for the filters only on selected slices. For example if 3D image has depth of 52 slices I want to apply Segmentation filters only from slice number 20 to slice number 30. How can I create an image out of these 10 slices so that I can apply Segmentation only on new image created out of these 10 slices image.

Thanks,
Jiten

#2

Perhaps this will do the trick

https://itk.org/Doxygen/html/classitk_1_1ExtractImageFilter.html

or this

https://itk.org/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html

2 Likes
#3

If you can identify to which files on disk do your slices of interest correspond to, you could copy only those slices into a new directory and open it as different image. This might, or might not be what you want to do.

#4

Thanks this may work I will try it out and provide my findings and observation s!

#5

Yup I would also need to save range of slices and a new image at later stage in post processing! Thanks

#6

Extract image filter does the trick!! Thanks much guys!!

#7

In SimpleITK it’s really easy to extract a subset of an image using python’s array slicing.

For example, this is how you could extract slice # 20:

import SimpleITK as sitk
image1 = sitk.Image(100,100,100,sitk.sitkUInt8)
image2 = image1[20]

or if you want to extract a range of slices:

image3 = image1[20:30]