[Insight-developers] GDCM Failure

[David Clunie]

The DICOM images appear to have been created by misuse of my
dicom3tools, perhaps during anonymization.

Specifically:

- there is an invalid root UID of 0.0.0.0 - the tools should be
   recompiled with an appropriate root in the configuration

- the study and series UIDs are not the same for the set - this
   can be achieved by using the -stamp option to dccp or similar,
   or by manually replacing (-r) these two UIDs with the UIDs
   from the first instance created

- several attributes have been removed when they should have been
   replaced with zero length (PatientBirthDate, ReferringPhysicianName,
   AccessionNumber)

David

Miller, James V (Research) wrote:
> Hans, 
> 
> Below is a diff between the DICOM tags in two of the files. The files have different
> Study UIDs.  When I load this directory into DICOMWorks, each image is shown as belonging
> to its own study.  What would you like GDCM to do with data? Are you expecting a 3D
> volume, a 4D volume? 
> 
> [200005014 at NSK1miller /c/projects/I2/castconvert_failed]$ /c/projects/I2/Insight-net2003/bin/relwithdebinfo/DicomImageReadPrintTags.exe anon_E3225S2I1.dcm > a
> [200005014 at NSK1miller /c/projects/I2/castconvert_failed]$ /c/projects/I2/Insight-net2003/bin/relwithdebinfo/DicomImageReadPrintTags.exe anon_E3225S2I2.dcm > b
> [200005014 at NSK1miller /c/projects/I2/castconvert_failed]$ diff a b
> 8c8
> < (0002|0003) Media Stored SOP Instance UID = 0.0.0.0.1.3225.2.1.1129047962.4645.18446744073701289826
> ---
> 
>>(0002|0003) Media Stored SOP Instance UID = 0.0.0.0.1.3225.2.2.1129047989.11790.18446744073701289826
> 
> 15c15
> < (0008|0013) Instance Creation Time = 112602
> ---
> 
>>(0008|0013) Instance Creation Time = 112629
> 
> 18c18
> < (0008|0018) SOP Instance UID = 0.0.0.0.1.3225.2.1.1129047962.4645.18446744073701289826
> ---
> 
>>(0008|0018) SOP Instance UID = 0.0.0.0.1.3225.2.2.1129047989.11790.18446744073701289826
> 
> 73,74c73,74
> < (0020|000d) Study Instance UID = 0.0.0.0.2.3225.1129047962.4645.18446744073701289826
> < (0020|000e) Series Instance UID = 0.0.0.0.3.3225.2.1129047962.4645.18446744073701289826
> ---
> 
>>(0020|000d) Study Instance UID = 0.0.0.0.2.3225.1129047989.11790.18446744073701289826
>>(0020|000e) Series Instance UID = 0.0.0.0.3.3225.2.1129047989.11790.18446744073701289826
> 
> 77,78c77,78
> < (0020|0012) Acquisition Number = 9218
> < (0020|0013) Image Number = 1 
> ---
> 
>>(0020|0012) Acquisition Number = 9219
>>(0020|0013) Image Number = 2 
> 
> 80,81c80,81
> < (0020|0030) Image Position (RET) = -115.500\-131.700\-83.5000
> < (0020|0032) Image Position Patient = -115.500\-131.700\-83.5000
> ---
> 
>>(0020|0030) Image Position (RET) = -115.500\-131.700\-82.0000
>>(0020|0032) Image Position Patient = -115.500\-131.700\-82.0000
> 
> 84c84
> < (0020|0052) Frame of Reference UID = 0.0.0.0.4.3225.2.1129047962.4645.18446744073701289826
> ---
> 
>>(0020|0052) Frame of Reference UID = 0.0.0.0.4.3225.2.1129047989.11790.18446744073701289826
> 
> 87c87
> < (0020|1041) Slice Location = -83.5000
> ---
> 
>>(0020|1041) Slice Location = -82.0000
> 
> 99c99
> < (0028|0107) Largest Image Pixel Value = 169
> ---
> 
>>(0028|0107) Largest Image Pixel Value = 221
> 
> 101,102c101,102
> < (0028|1050) Window Center = 84
> < (0028|1051) Window Width = 169 
> ---
> 
>>(0028|1050) Window Center = 110 
>>(0028|1051) Window Width = 221 
> 
> 
> -----Original Message-----
> From: insight-developers-bounces+millerjv=crd.ge.com at itk.org
> [mailto:insight-developers-bounces+millerjv=crd.ge.com at itk.org]On Behalf
> Of Hans Johnson
> Sent: Tuesday, October 11, 2005 2:09 PM
> To: mathieu.malaterre at kitware.com; insight-developers at itk.org
> Subject: [Insight-developers] GDCM Failure
> 
> 
> Matheiu (and others),
> 
> Our group is attempting to use the ITK/GDCM components to convert dicom 
> images to the newly added nifti format using the cast convert program.  
> For the most part, this works very well, but there is a failure in 
> making the dicom file list from a directory for some types of data.
> 
> 
> I have an example data set that causes GDCM to fail:
> http://www.psychiatry.uiowa.edu/users/hjohnson/castconvert_failed.tar.gz
> 
> 
> This same data set can be converted to nifti file format with the afni 
> to3d tool, and with the BRAINS file readers/writers.
> 
> Any help or advice would be greatly appreciated.
> 
> Hans
> 
> 
> 
> 
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