[Insight-users] Incorrect origin and spacing when converting DICOM to metaimage

Mengda Wu wumengda at gmail.com
Mon Nov 11 10:22:24 EST 2013


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/DicomSeriesReadImageWrite2.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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