CODEWITHSUNDEEP
bioinformaticsmedicalmedical-imaging
NUI
NUI

Reputation: 23

How can Nifti files be restructured so that they can be fitted in a CNN?

Most of my Nifti files have different xyZ dimensions. How can I arrange them so that they have the same dimensionality and then be able to train them in a CNN?

Upvotes: 1

Views: 343

Answers (1)

Robbie
Robbie

Reputation: 4882

You can resample the images to have the same voxel size and then crop them to cover the same physical size. This is important because if you just re-size the images then each pixel (or voxel in 3D) will be a different physical size, and your CNN will be learning features at different scales.

If you are interested in performing this in Python, then I strongly suggest SimpleITK. Another package built on top of this is platipy - which has tools for isotropic resampling and cropping which could be useful.

Upvotes: 2

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