Dicom images fail to read

Community VMTK
1

Hello all,

I’m a new user of VMTK, trying to read in a set of processed DICOM images with the command “vmtkimagereader -ifile C:\Users\Admin\Documents\s0.5-10\1 -f dicom”. When I do so, it produces the following error:
Traceback (most recent call last):
File “C:\Users\Admin\miniforge3\envs\vmtk\lib\site-packages\vmtk\pypeserver.py”, line 46, in RunPypeProcess
pipe.Execute()
File “C:\Users\Admin\miniforge3\envs\vmtk\lib\site-packages\vmtk\pype.py”, line 324, in Execute
scriptObject.Execute()
File “C:\Users\Admin\miniforge3\envs\vmtk\lib\site-packages\vmtk\vmtkimagereader.py”, line 266, in Execute
self.ReadITKIO()
File “C:\Users\Admin\miniforge3\envs\vmtk\lib\site-packages\vmtk\vmtkimagereader.py”, line 203, in ReadITKIO
matrix.GetElement(0,0), matrix.GetElement(0,1), matrix.GetElement(0,2), matrix.GetElement(0,3),
AttributeError: ‘NoneType’ object has no attribute ‘GetElement’

as well as the following, in the pypepad output:

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I’ve tried importing multiple different sets of DICOM images, both those I am working with and test datasets, on two different PCs (Windows 10/11), with both binary installation versions as well as through conda forge. Any help in resolving this issue would be greatly appreciated.

2

Is there a reason why you are not using the Slicer’s DICOM module?

4

I’m trying to use VMTK standalone (hence why I posted under the VMTK community).

5

Just in case you have been tasked by doctors to press the juice from a DICOM series in one click, please consider it is impossible.

You may automate a lot of tasks if you use Slicer itself, that’s the way to go and it won’t ever be one-click-get-all.

Admittedly, your purpose may be something else and my comments are unrelated to your intent. Nevertheless, I still point out that it’s not fun playing with VMTK standalone.

6

Sorry don’t know anything about standalone VMTK. All I know, as @chir.set is alluded DICOM is a complicated format, and developers of Slicer has put a lot of effort into building a robust DICOM module that handles myriads of exceptions and oddities vendors provide.

Hope someone on the forum can help you with your question.

7

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I seem to have attached the wrong image, I’ve just noticed. The error is roughly the same but the path is to an actual DICOM image.

8

In noticing this I’ve discovered why I’m getting this error: in all cases either the directory I was working in began with a python escape character, or my images began with a number (causing the same effect). Adding an extra slash has prevented the error (though the image viewer now appears to be showing an entirely black volume).