Re: [itksnap-users:1051] URGENT (work in progress): ITK Snap crashes randomly trying to load a DICOM File

[Paul Yushkevich]

Hi Stefan

The reason SNAP crashes with this image is that the image does not seem to encode a proper 3D coordinate system. SNAP expects every image format to describe the spatial direction of the three image coordinate axes (rows of pixels, columns of pixels, slices) and those spatial directions are assumed to be orthogonal. That does not seem to be so in the header of the DICOM file.

I was able to load your image into SNAP by using the following C3D command (itksnap.org/c3d)

c3d Example1.IMA -info -orient AIL -o test.nii.gz

Image #1: dim = [192, 192, 1];  bb = {[29.0293 -169.172 165.896], [329.029 130.828 175.896]};  vox = [1.5625, 1.5625, 10];  range = [0, 653];  orient = Oblique, closest to ASA

The output of the command, with highlight above, shows that the program thinks that the image has an ASA orientation, i.e., the x axis and the z axis both go from Anterior to Posterior, and this causes SNAP to crash.

C3D is not very good at DICOM I/O, it works for this single slice DICOM file, but might not for series of DICOM images. I would also try using dcm2nii from mricron to convert DICOM to NIFTI, and then apply the -orient command to the NIFTI image.

I need to add some code to catch problems with images like these to report to the user that there was a problem.

Paul.

On Sat, Mar 30, 2013 at 7:29 AM, <stefan.co...@gmail.com> wrote:

 

Hello to everybody.

My problem: ITK Snap crashes trying to load a DICOM file. I am using the wizard for loading a greyscale image and exactly after clicking on "finish" at the end of the process ITK Snap crashes. I am not able to find an explanation for this, the problem seems to occur randomly with different DICOM files. I am using Windows 7 Professional 64 bit and the ITK SNAP 64 bit version. I have tried to use ITK SNAP 32 bit under Windows XP Mode, but this doesn't change a thing. I added an example DICOM file to my post.

I would be very glad for any help you can offer in solving this problem as I am currently working on a project with ITK SNAP.

Thanks a lot
Stefan Colling

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania