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

[John Drozd]

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