[Insight-developers] GDCM Failure

[Hans Johnson]

David,

Thanks for you help.  I've applied for a UID for our site, made 
consistent study and series UID's, and made the specified fields 
included with zero length.

IT WORKS!!

Thanks,
Hans

David Clunie wrote:

> 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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