[ITK Community] [Insight-developers] Incorrect origin and spacing when converting DICOM to metaimage
Williams, Norman K
norman-k-williams at uiowa.edu
Mon Nov 11 10:40:43 EST 2013
Try using DCMTKImageIO instead. This needs to be turned on when you
configure and build ITK.
Module_ITKDCMTK:BOOL=ON
Module_ITKIODCMTK:BOOL=ON
GDCM has some issues with reading DICOM files. These may or may not be
addressed with a more recent version of GDCM; the last time I tried using
a current version of GDCM I couldn't get ITK to build with it.
--
Kent Williams norman-k-williams at uiowa.edu
On 11/11/13 9:22 AM, "Mengda Wu" <wumengda at gmail.com> wrote:
>BTW, here is what I got by running gdcminfo (gdcm version 2.4.0) on one
>of the dicoms:
>======================================================================
>MediaStorage is 1.2.840.10008.5.1.4.1.1.7 [Secondary Capture Image
>Storage]
>TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
>NumberOfDimensions: 2
>Dimensions: (512,512,1)
>SamplesPerPixel :1
>BitsAllocated :16
>BitsStored :16
>HighBit :15
>PixelRepresentation:1
>ScalarType found :INT16
>PhotometricInterpretation: MONOCHROME2
>PlanarConfiguration: 0
>TransferSyntax: 1.2.840.10008.1.2.1
>Origin: (0,0,0)
>Spacing: (1,1,1)
>DirectionCosines: (1,0,0,0,1,0)
>Rescale Intercept/Slope: (-1024,1)
>Orientation Label: AXIAL
>=======================================================================
>
>
>Clearly, from
>(0018,0088)=0.449999988
>
>(0028,0030)=0.400391012\0.400391012
>
>The spacing should not be (1,1,1).
>
>Thanks,
>Mengda
>
>
>
>
>
>On Mon, Nov 11, 2013 at 10:14 AM, Mengda Wu
><wumengda at gmail.com> wrote:
>
>Hi all,
>
> I have some dicom images in my new project. But when I tried to convert
>them to the ITK metaimages, the origin and spacing are incorrect even
>though the intensities are right. The origin becomes (0,0,0) and spacing
>is (1,1,1). I am the example
>DicomSeriesReadImageWrite2.cxx
><http://itk.org/gitweb?p=ITK.git;a=blob_plain;f=Examples/IO/DicomSeriesRea
>dImageWrite2.cxx;hb=HEAD>
>
>
>
>from ITK 4.4.2. The code does not have any issue with other Dicoms for my
>previous projects. so my guess is the current dicoms miss some fields in
>the header that ITK needs.
>
>
>Can you help? I am attaching the fields from one dicom as follows:
>
>(0002,0000) Group Length
>Value: 206
>(0002,0001) File Meta Information Version
>Value: 0
>(0002,0002) Media Storage SOP Class UID
>Value: 1.2.840.10008.5.1.4.1.1.7
>(0002,0003) Media Storage SOP Instance UID
>Value: 1.2.276.0.28.3.2418833.1095761920.42.5040.2012041216272628700
>(0002,0010) Transfer Syntax UID
>Value: 1.2.840.10008.1.2.1
>(0002,0012) Implementation Class UID
>Value: 1.2.276.0.7230010.3.0.3.6.0
>(0002,0013) Implementation Version Name
>Value: OFFIS_DCMTK_360
>
>(0008,0008) Image Type
>Value: DERIVED\SECONDARY\REFORMATTED
>
>(0008,0016) SOP Class UID
>Value: 1.2.840.10008.5.1.4.1.1.7
>(0008,0018) SOP Instance UID
>Value: 1.2.276.0.28.3.2418833.1095761920.42.5040.2012041216272628700
>(0008,0020) Study Date
>(0008,0022) Acquisition Date
>Value: 20120116
>(0008,0023) Image Date
>Value: 20120116
>(0008,0030) Study Time
>(0008,0033) Image Time
>Value: 120859.658000
>
>(0008,0050) Accession Number
>(0008,0060) Modality
>Value: CT
>(0008,0070) Manufacturer
>Value: Philips
>
>(0008,0080) Institution Name
>Value: Hide
>(0008,0090) Referring Physician's Name
>(0008,103E) Series Description
>Value: Hide
>(0008,1090) Manufacturer's Model Name
>Value: Brillance 64
>(0010,0010) Patient's Name
>Value: Patient00
>(0010,0020) Patient ID
>(0010,0030) Patient's Birth Date
>Value: NewDOB16
>(0010,0040) Patient's Sex
>Value: F
>(0010,1010) Patient's Age
>Value: 054Y
>(0018,0088) Spacing Between Slices
>Value: 0.449999988
>
>(0018,1151) X-ray Tube Current
>Value: 429
>(0020,000D) Study Instance UID
>Value: 1.2.276.0.28.3.2418833.1095761920.42.3628.2012011611085965900
>(0020,000E) Series Instance UID
>Value: 1.2.276.0.28.3.2418833.1095761920.42.3628.2012011611085965901
>(0020,0010) Study ID
>(0020,0011) Series Number
>(0020,0013) Image Number
>Value: 1
>(0020,0020) Patient Orientation
>(0020,0032) Image Position (Patient)
>Value: 0.200195506\0.200195506\0.224999994
>
>(0020,0037) Image Orientation (Patient)
>Value: 1\0\0\0\1\0
>
>(0020,4000) Image Comments
>(0021,0010)
>Value: Timepoint Information
>
>(0021,1010)
>Value: 20120116 120608.154000
>(0021,1011)
>Value: UNKNOWN
>
>(0028,0002) Samples per Pixel
>Value: 1
>(0028,0004) Photometric Interpretation
>Value: MONOCHROME2
>
>(0028,0008) Number of Frames
>Value: 1
>(0028,0010) Rows
>Value: 512
>(0028,0011) Columns
>Value: 512
>(0028,0030) Pixel Spacing
>Value: 0.400391012\0.400391012
>
>(0028,0100) Bits Allocated
>Value: 16
>(0028,0101) Bits Stored
>Value: 16
>(0028,0102) High Bit
>Value: 15
>(0028,0103) Pixel Representation
>Value: 1
>(0028,0106) Smallest Image Pixel Value
>Value: 0
>(0028,0107) Largest Image Pixel Value
>Value: 2610
>(0028,1050) Window Center
>Value: 150
>(0028,1051) Window Width
>Value: 500
>(0028,1052) Rescale Intercept
>Value: -1024
>(0028,1053) Rescale Slope
>Value: 1
>
>
>
>
>Thanks,
>Mengda
>
>
>
>
>
>
>
>
>
>
>
>
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