How to get pixel value and coordinate from nrrd file

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1

So I make nrrd file. In this file has Annotation Data using 3D Slicer.

I want to get pixel coordinate and pixel value from this file.

I modified the code with reference to the source of this link, but I did not get any results.

python dicom – getting pixel value from dicom file

I really couldn’t find any information so any helpful resources would be appreciated as well. Thank you.

2

These examples in the script repository should help:

https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Modify_voxels_in_a_volume

https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Get_volume_voxel_coordinates_from_markup_fiducial_RAS_coordinates

https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Get_markup_fiducial_RAS_coordinates_from_volume_voxel_coordinates

3

Thanks reply.

This code need to use python interaction in 3D Slicer. Right??

4

You need to run the code in Slicer’s Python environment. You probably don’t need to show Slicer GUI - you can run your script from the command-line.

5

Oh I can see array!

And i want to know each array’s all information.

now we can see like this.
[[[0 0 0 …, 0 0 0]
[0 0 0 …, 0 0 0]
[0 0 0 …, 0 0 0]

i want to remove … this part and i want to print all arrya elements.

and i save result to txt file. but result is same.

image
image719×413 5.2 KB

6

Writing out 3D volume to text file is a bad idea (large file, slow to read/write, potential data loss due to limited precision), but here is a complete example just to show how easy it is to do:

# Get some image data
import SampleData
volumeNode=SampleData.SampleDataLogic().downloadMRHead()

# Get voxels as numpy array
volumeArray=slicer.util.arrayFromVolume(volumeNode)

# Write voxels to text file
import numpy as np
with file('c:/tmp/test.txt', 'w') as outfile:
  for data_slice in volumeArray:
    np.savetxt(outfile, data_slice, fmt='%-7.2f')

If you want to write in a different format then search for Python code examples on the web.