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

Fri Nov 27 12:31:55 EST 2009

Hi all,

I originally have a dicom series of 2d slices which I had converted to a 3D
dicom volume for processing.
I'll try processing the dicom series and then write the output to a dicom
series of 2d slices, to see if I can circumvent this problem.
I'll let you know if this works?

I'll provide a link to my data as well, but it probably won't be until the
weekend.

Thanks,
john

On Fri, Nov 27, 2009 at 12:23 PM, Mathieu Malaterre <
mathieu.malaterre at gmail.com> wrote:

> 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
> >>
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.html
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://www.itk.org/mailman/listinfo/insight-users
> >
>
>
>
> --
> Mathieu
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20091127/bff4708e/attachment-0001.htm>