Tumor segmentation

Support
1

I tried to segment the tumor but when I save it as .nrrd, I got the whole volume with other tissues. I want to save and use JUST the tumor volume. how can I do that?

Do I have to use the Editor to segment the tumor or I can do something by CLI?

2

Hide all segments that you don’t want to export and in advanced section of Export section, choose Visible segments only.

3

Thank you it works and I got (segmentation.seg.nrrd and segmentation-lable.nrrd)

However, since I’m new learner, I want to get the volume (segmented tumor) as an array.

so I loaded the “segmentation-lable.nrrd” then:

o= slicer.util.array(‘segmentation-lable’)
print (o)
[[[0 0 0 …, 0 0 0]
[0 0 0 …, 0 0 0]
[0 0 0 …, 0 0 0]
…

I’m getting zeros
Could you please guide me

Thank you.

4

It may look like zeros, but your data is probably just being shortened for display.

Try o.max() and you should see the label value you exported.

Also something like:

import numpy
numpy.transpose(numpy.where(o==1))

will give you a list of the pixel coordinates where there’s a 1 in the segmentation array.

HTH

5

now I got “None” when printing o

6

You got None if you mistype the node name or the image is invalid.

I would recommend to use slicer.util.arrayFromSegment(). It can retrieve voxels directly from segmentation node, you don’t need to export it to labelmap.

7

now I’m getting error.
Could you please give me the complete steps code maybe I did something wrong.

8

Sorry, I need more specific information than this to be able to help.

You can get help on usage of any commands by using help command. For example: help(slicer.util.arrayFromSegment).

See complete example here: Area of segment in a given slice? - #3 by lassoan