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

[Bill Lorensen]

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
>