[Elastix] Image Orientation Challenges Continued

Tue Aug 15 00:55:25 CEST 2017


I have a large number of images that I want to register to a single template so I can compare them to each other. Each of these DICOM images may have different orientation information, so I had included the parameter (UseDirectionCosines "true"). However, I was receiving the following error when I run elastix:

Error: In /build/gdcm-2.4.4/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx, line 586, function static std::vector<double> gdcm::ImageHelper::GetDirectionCosinesValue(const gdcm::File&)
Image Orientation (Patient) was not found

Per Stefan Klein's suggestion, I incorporated an additional step to convert the DICOMs to NIFTIs with dcm2niix prior to registration. The error no longer appears, but my results are still problematic. In some cases, it looks as though the registration was attempted between an upside-down version of my image and the template. In these cases, when I flip the image data in a python script (and leave the header information as is), the registration appears to work as intended.

I'm trying to isolate the problem. Is elastix misinterpreting the image orientation? Is dcm2niix mishandling the orientation during the conversion? Or is the problem outside of either of these programs? How do I find out?

Any ideas would be appreciated. Thanks!

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