Get each slice of a volume as numpy array

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1

Hi Andras,
Would you please tell me how to split the volume into slices after having volume into numpy array?

What I need to do is to apply clustering FCM algorithm on volume to get classified volume. For which I am thinking in this way.
Get the volume
Split it into slices
convert each slice into its respective numpy array
passing numpy array of a slice to algorithm
Getting the updated numpy array
converting numpy back to slice of volume
Then collectivly combining all the slices into volume

Thank you

Looking forward for your reply

2

You can easily get a slice of a volume by standard numpy indexing of arrays. Here is an example: https://gist.github.com/lassoan/d85be45b7284a3b4e580688fccdb1d02

However, I would recommend to segment in 3D rather than arbitrarily splitting the volume to 2D pieces and re-assembling it.

1 Like
3

Hi Andras,
Thank you for suggesting. Please tell where should I start from if I want to do 3D segmentation.

Regards,
Saima Safdar

4

What would you like to segment? On what imaging modality? For what clinical purpose?

5

Hi,
want to segment three parts brain, ventricles and tumor, MRI. automating the segmentation process and then using it for brain deformation calculation.