Set Photometric Interpretation for GDCMImageIO as MONOCHROME2 in SimpleITK

Beginner Questions
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1

I am trying to read diffusion MRI scans using SimpleITK in Python. I am using the ImageFileReader with the GDCMImageIO interface. In the DICOM header the tag (0028, 0004) Photometric Interpretation is set as MONOCHROME1. So when I execute the reader I have inverted images. Is there a way to make the GDCMImageIO set the photometric interpretation at MONOCHROME2?

2

What version of SimpleITK are you using? This may have been fixed in ITK recently. Please try SimpleITK 2.0rc1 to see if the issue still exists.

3

Thanks for the quick response!

I am currently using SimpleITK 2.0rc1

5

Hello @theo-barfoot,
This is an ITK decision see here,

Ad-hoc solution:

photometric_interpretation = image_file_reader.GetMetaData('0028|0004').strip()
if photometric_interpretation == 'MONOCHROME1':
    image = -image + max_value
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6

Thanks for the solution zivy!

Is there perhaps a way to modify the behaviour of the GDCMImageIO from Python?

I noticed in your link to the C++ code that there is a method called: “SetPhotometricInterpretation”. Is there a way to invoke this from the python code?

7

Hello @theo-barfoot,

Unfortunately that is a gdcm method which is not exposed by ITK, so no.

8

Using your ad-hoc work around I unfortunately get: ERROR: Pixel type: 16-bit unsigned integer is not supported in 3D byN3itk6simple21UnaryMinusImageFilterE

However, I have managed to modify the code very slightly and it works just fine:

photometric_interpretation = reader.GetMetaData('0028|0004').strip()
if photometric_interpretation == 'MONOCHROME1':
    image = image*-1 + max(image)

An alternative for me is just to edit the PhotometricInterpretation DICOM tag to be MONOCHROME2 before reading it with SimpleITK.

Thanks for your help!

9

I would recommend the following ( untested code ):

mmFilter = sitk.MinimumMaximumImageFilter()
mmFilter.Execute(image)
image = sitk::InvertIntensity(image, maximum=mmFilter.GetMaximum())

This uses a fast filter as opposed to image iterators that max uses. And uses the InvertIntensity filter so that you are not doing funky negative multiplication with an unsigned integer.

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10

Thanks, works great!