[Elastix] Image Orientation (Patient) was not found

Wed Aug 2 05:27:56 CEST 2017

Hi Yuxuan,

I was on a Debian machine when I got the error but it worked fine on my Mac. Apparently the Debian version was 4.7 and my Mac version was 4.8, but I'm unsure if that is the root cause.
Also peculiar was that though I received the error on one and not the other, the output from them appeared identical.

But just to be safe, I followed Stefan's advice and converted to NIFTI prior to registration using dcm2niix. Unfortunately I do not know of any scripts that convert to .mhd.

Good luck!


From: elastix-bounces at bigr.nl <elastix-bounces at bigr.nl> on behalf of Yuxuan Cheng <yxcheng at uw.edu>
Sent: Tuesday, August 1, 2017 9:07:15 PM
To: elastix at bigr.nl
Subject: Re: [Elastix] Image Orientation (Patient) was not found

Hi Lindsay,

I got same issue on Linux but the software worked well on Windows.
How do you solve the issue? Or do you know any scripts can convert dicom to .mhd file? Thank you!


On Thu, Jul 13, 2017 at 1:32 AM, S. Klein <s.klein at erasmusmc.nl<mailto:s.klein at erasmusmc.nl>> wrote:

Hi Lindsay,

I think it's best if you first convert the DICOM to a simpler format like .nii or .mhd. In that conversion you can deal with all the exceptions for DICOM files for different scanners. Support for reading DICOM files/directories is very limited in Elastix itself.

Best, Stefan

On 12-07-2017 20:03, Quandt, Lindsay M wrote:

Hi everyone,

I am attempting to register an image with (UseDirectionCosines "true"). However, when I perform the registration, I receive this error:

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

After inspection, I know my input DICOM image contains values for the IOP so I don't think this should be an issue. I believe default values are used in absence of the true direction cosines, but I don't want the defaults.

Any thoughts would be appreciated. Thanks!


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Stefan Klein
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Yuxuan Cheng
PhD student,
Department of Bioengineering ,
University of Washington,
Seattle, WA 98195, USA
Email: yxcheng at uw.edu<mailto:yxcheng at uw.edu>
Homepage: https://sites.google.com/view/ycheng
Tel: 1 (206) 739 6555

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