[Insight-users] problem with orientation of dicom output from segmentation

Fri Nov 27 12:23:26 EST 2009

This is a post ITK 3.16 feature I am afraid:

http://www.cmake.org/Bug/view.php?id=7748

(0017626)
Mathieu.Malaterre (developer)
2009-09-19 06:51

	This will be post ITK 3.16.

Thanks for the patch ! Sorry for being so long to fix it.

On Fri, Nov 27, 2009 at 6:11 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> John,
>
> 3.16 will not help. This looks like a bug for sure.
>
> Can you provide a link to a dataset that we can use to reproduce the
> problem? We don't have much experience with 3D dicom files I'm afraid.
>
> Bill
>
> On Fri, Nov 27, 2009 at 11:59 AM, John Drozd <john.drozd at gmail.com> wrote:
>> Hi Bill,
>>
>> I am currently using the ITK 3.14 that is in the 3D Slicer 3.4
>> directory Slicer3-lib/Insight
>>
>> If I upgrade to ITK 3.16, will this solve my problem?
>>
>> I downloaded ITK 3.16 and noticed using the diff command that
>> itkGDCMIO.h has been modified from what it was in ITK 3.14.
>>
>> But when I ran diff on gdcmOrientation.cxx in both versions of ITK,
>> diff showed no difference.
>>
>> John
>>
>> On Friday, November 27, 2009, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>> John,
>>>
>>> What version of itk are you using? Are you using the gdcm 1.x that is
>>> in the itk source tree or an external gdcm 2.x version?
>>>
>>> Bill
>>>
>>> On Thu, Nov 26, 2009 at 3:22 PM, John Drozd <john.drozd at gmail.com> wrote:
>>>> Hi Luis,
>>>>
>>>> I was getting a segmentation fault because I had forgotten to change the
>>>> Dimension from 2 to 3 in DicomReadPrintTag.cxx.
>>>>
>>>> For the input image, I have:
>>>> (0020|0037) Image Orientation (Patient) = 0.0\0.0\-1.0\0.0\1.0\0.0
>>>>
>>>> For the output image, I have:
>>>> (0020|0037) Image Orientation (Patient) =
>>>> 0.000000\0.000000\1.000000\0.000000\1.000000\0.000000
>>>>
>>>> There is a difference.  Since the program is changing the orientation when
>>>> processed through the pipeline, is the best approach to manually change the
>>>> orientation tag of the dictionary and then copy the revised dictionary to
>>>> the output file?
>>>>
>>>> john
>>>>
>>>> Below are the full tags:
>>>>
>>>> [jdrozd at trumpet DicomImageReadPrintTags]$ ./DicomImageReadPrintTags
>>>> correctedsubject5.dcm
>>>> (0002|0000) Group Length =
>>>> 214
>>>> (0002|0001) File Meta Information Version =
>>>> AAE=
>>>> (0002|0002) Media Storage SOP Class UID =
>>>> 1.2.840.10008.5.1.4.1.1.2
>>>> (0002|0003) Media Storage SOP Instance UID =
>>>> 1.2.826.0.1.3680043.2.1125.1.10607669833050788267094246636093811
>>>> (0002|0010) Transfer Syntax UID =
>>>> 1.2.840.10008.1.2.1
>>>> (0002|0012) Implementation Class UID =
>>>> 147.144.143.155
>>>> (0002|0013) Implementation Version Name = ITK/GDCM
>>>> 1.2.4
>>>> (0002|0016) Source Application Entity Title =
>>>> NOTSPECIFIED
>>>> (0008|0008) Image Type =
>>>> DERIVED\PRIMARY
>>>> (0008|0012) Instance Creation Date =
>>>> 20091029
>>>> (0008|0013) Instance Creation Time =
>>>> 135224
>>>> (0008|0016) SOP Class UID =
>>>> 1.2.840.10008.5.1.4.1.1.2
>>>> (0008|0018) SOP Instance UID =
>>>> 1.2.826.0.1.3680043.2.1125.1.10607669833050788267094246636093811
>>>> (0008|0020) Study Date =
>>>> 20081030
>>>> (0008|0030) Study Time =
>>>> 164348.940
>>>> (0008|0050) Accession Number
>>>> =
>>>> (0008|0060) Modality =
>>>> CT
>>>> (0008|0064) Conversion Type =
>>>> WSD
>>>> (0008|0070) Manufacturer =
>>>> Manifacturer
>>>> (0008|0080) Institution Name = GDCM
>>>> Hospital
>>>> (0008|0090) Referring Physician's Name = Refering
>>>> Phisician
>>>> (0010|0010) Patient's Name = Patient
>>>> 188858520
>>>> (0010|0020) Patient ID =
>>>> 1747233212
>>>> (0010|0030) Patient's Birth Date =
>>>> 19500101
>>>> (0010|0040) Patient's Sex =
>>>> M
>>>> (0018|0088) Spacing Between Slices =
>>>> 1.207500
>>>> (0018|1164) Imager Pixel Spacing =
>>>> 0.945750\0.945750
>>>> (0020|000d) Study Instance UID =
>>>> 1.2.826.0.1.3680043.2.1125.1.53653479342656887425609263146205769
>>>> (0020|000e) Series Instance UID =
>>>> 1.2.826.0.1.3680043.2.1125.1.47155241092896696198844159625679986
>>>> (0020|0010) Study ID =
>>>> 1533117581
>>>> (0020|0011) Series Number =
>>>> 2135500125
>>>> (0020|0013) Instance Number =
>>>> 165
>>>> (0020|0020) Patient Orientation =
>>>> L\P
>>>> (0020|0032) Image Position (Patient) =
>>>> 199.237496852874\0.0\0.0
>>>> (0020|0037) Image Orientation (Patient) =
>>>> 0.0\0.0\-1.0\0.0\1.0\0.0
>>>> (0020|4000) Image Comments = NOT FOR CLINICAL
>>>> USE
>>>> (0028|0002) Samples per Pixel =
>>>> 1
>>>> (0028|0004) Photometric Interpretation =
>>>> MONOCHROME2
>>>> (0028|0008) Number of Frames =
>>>> 166
>>>> (0028|0010) Rows =
>>>> 256
>>>> (0028|0011) Columns =
>>>> 256
>>>> (0028|0030) Pixel Spacing =
>>>> 0.945750\0.945750
>>>> (0028|0034) Pixel Aspect Ratio =
>>>> 1\1
>>>> (0028|0100) Bits Allocated =
>>>> 16
>>>> (0028|0101) Bits Stored =
>>>> 16
>>>> (0028|0102) High Bit =
>>>> 15
>>>> (0028|0103) Pixel Representation =
>>>> 0
>>>> (0028|1052) Rescale Intercept =
>>>> 0.0
>>>> (0028|1053) Rescale Slope =
>>>> 1.0
>>>> (0028|1054) Rescale Type =
>>>> US
>>>> (7fe0|0000) Group Length =
>>>> 21757964
>>>> Patient's Name (0010|0010)  is: Patient
>>>> 188858520
>>>> Performing Physician's Name (0008|1050): (No Value Found in
>>>> File)
>>>> PixelType:
>>>> scalar
>>>> Component Type: unsigned_short
>>>>
>>>> [jdrozd at trumpet DicomImageReadPrintTags]$ ./DicomImageReadPrintTags
>>>> outsubject5.dcm
>>>> (0002|0000) Group Length =
>>>> 194
>>>> (0002|00
>>
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-- 
Mathieu