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

[Mathieu Malaterre]

3D Multi-Frames images are very poorly supported in GDCM 1.2.x.
gdcmOrientation.cxx does not contains this information. It is meant to
compute the likley orientation of the image (Axial, Coronal. ...)

HTH

On Fri, Nov 27, 2009 at 5:59 PM, 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