[vtkusers] Different Image bounds ITK-VTK Image Export

somi seesomi at gmail.com
Tue Sep 18 14:41:27 EDT 2012


Hi,
I have an application where I read a dicom series, export it to VTK and
display it using vtkImageViewer2.
The problem is that when the DICOM has a gantry tilt, the exported VTK
Image data doesn't have the same
co-ordinates at the ITK image. Specifically the image bounds are different.

I created a small test program which loads DICOM data and displays the ITK
and VTK image info.
The output is shown below. Test_Data_A has gantry tilt while Test_Data_B
doesn't.
As you can see from the output below, the image bounds for Test_Data_B
match for ITK
and VTK while the don't for Test_Data_A. Do I have to manually apply the
tilt transform
to VTK image after exporting ?
The test program along with data to reproduce the problem can be downloaded
from http://somesh.be/files/testData/Test_Program_Data.tar.gz
I have also attached the dicom header for the first image ins the series
for both data.
Each has 3 slices.

Usage: itkVtkTest DICOM_DIR

Output of program for Test_Data_A with gantry tilt
 Opening Dicom DIR ../Test_Data_A
 ITK: Image Origin (16.7662 , -86.2766 , -59.2801 )
 ITK: Image Spacing (0.332031 , 0.332031 , 2 )
 ITK: Image Dimensions (512 , 512 , 3 )
 ITK: Image Bounds :
  X :[ 16.7662 , 13.8201 ]
  Y :[ -86.2766 , 83.4128 ]
  Z :[ -59.2801 , -228.948 ]
 VTK: Image Origin (16.7662 , -86.2766 , -59.2801 )
 VTK: Image Spacing (0.332031 , 0.332031 , 2 )
 VTK: Image Dimensions (512 , 512 , 3 )
 VTK: Image Bounds :
  X :[ 16.7662 , 186.434 ]
  Y :[ -86.2766 , 83.3912 ]
  Z :[ -59.2801 , -55.2801 ]


Output of program for Test_Data_B with NO gantry tilt
 Opening Dicom DIR ../Test_Data_B
 ITK: Image Origin (-227 , -137 , -1381.1 )
 ITK: Image Spacing (0.855469 , 0.855469 , 1.29993 )
 ITK: Image Dimensions (512 , 512 , 3 )
 ITK: Image Bounds :
  X :[ -227 , 210.145 ]
  Y :[ -137 , 300.145 ]
  Z :[ -1381.1 , -1378.5 ]
 VTK: Image Origin (-227 , -137 , -1381.1 )
 VTK: Image Spacing (0.855469 , 0.855469 , 1.29993 )
 VTK: Image Dimensions (512 , 512 , 3 )
 VTK: Image Bounds :
  X :[ -227 , 210.145 ]
  Y :[ -137 , 300.145 ]
  Z :[ -1381.1 , -1378.5 ]

I have also posted this in ITK mailing list.


Thanks,
Somi
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 0008,0005 *                Specific Character Set          CS [  10 bytes] ISO_IR 100
 0008,0008 *                            Image Type          CS [  38 bytes] DERIVED\SECONDARY\REFORMATTED\AVERAGE 
 0008,0012 *                Instance Creation Date          DA [   8 bytes] 20120911
 0008,0013 *                Instance Creation Time          TM [   6 bytes] 094316
 0008,0016 *                         SOP Class UID          UI [  26 bytes] 1.2.840.10008.5.1.4.1.1.2
 0008,0018 *                      SOP Instance UID          UI [  50 bytes] 1.2.840.113619.2.80.1943250916.23991.1347374596.10...
 0008,0020 *                            Study Date          DA [   8 bytes] 20120911
 0008,0021 *                           Series Date          DA [   8 bytes] 20120911
 0008,0022 *                      Acquisition Date          DA [   8 bytes] 20120911
 0008,0023 *                            Image Date          DA [   8 bytes] 20120911
 0008,0030 *                            Study Time          TM [   6 bytes] 093259
 0008,0031 *                           Series Time          TM [   6 bytes] 094314
 0008,0032 *                      Acquisition Time          TM [  14 bytes] 093543.342370 
 0008,0033 *                            Image Time          TM [   6 bytes] 094316
 0008,0050 *                      Accession Number          SH [   8 bytes] 6428434 
 0008,0060 *                              Modality          CS [   2 bytes] CT
 0008,0070 *                          Manufacturer          LO [  18 bytes] GE MEDICAL SYSTEMS
 0008,0080 *                      Institution Name          LO [   6 bytes] ANNOYN
 0008,0090 *                   Referring Physician          PN [   6 bytes] ANNOYN
 0008,1010 *                          Station Name          SH [   6 bytes] ANNOYN
 0008,1030 *                     Study Description          LO [   6 bytes] ANNOYN
 0008,103E *                    Series Description          LO [   6 bytes] ANNOYN
 0008,1050 *           Performing Physician's Name          PN [   4 bytes] ^^^^
 0008,1070 *                       Operator's Name          PN [   6 bytes] ANNOYN
 0008,1090 *             Manufacturer's Model Name          LO [  12 bytes] BrightSpeed 
 0010,0010 *                        Patient's Name          PN [   6 bytes] ANNOYN
 0010,0020 *                            Patient ID          LO [   6 bytes] ANNOYN
 0010,0030 *                   Patient's Birthdate          DA [   6 bytes] ANNOYN
 0010,0040 *                         Patient's Sex          CS [   6 bytes] ANNOYN
 0010,1000 U             General, but not defined.          -- [   0 bytes] 
 0010,1010 *                         Patient's Age          AS [   6 bytes] ANNOYN
 0010,1020 *                        Patient's Size          DS [   6 bytes] ANNOYN
 0018,0022 *                          Scan Options          CS [  12 bytes] HELICAL MODE
 0018,0050 *                  Slice Thickness (mm)          DS [   2 bytes] 2 
 0018,0060 *                        Peak kilovolts          DS [   4 bytes] 120 
 0018,0090 *              Data Collection Diameter          DS [  10 bytes] 500.000000
 0018,1016 U             General, but not defined.          -- [  18 bytes] 
 0018,1018 U             General, but not defined.          -- [  14 bytes] 
 0018,1019 U             General, but not defined.          -- [   6 bytes] 
 0018,1020 *                   Software Version(s)          LO [   6 bytes] mach.4
 0018,1030 *                         Protocol Name          LO [   6 bytes] ANNOYN
 0018,1110 *           Distance Source to Detector          DS [  10 bytes] 949.075000
 0018,1111 *            Distance Source to Patient          DS [  10 bytes] 541.000000
 0018,1130 *                          Table Height          DS [  10 bytes] 123.000000
 0018,1140 *                    Rotation Detection          CS [   2 bytes] CW
 0018,1150 *                         Exposure Time          IS [   4 bytes] 478 
 0018,1151 *                    X-ray Tube Current          IS [   4 bytes] 437 
 0018,1152 *                              Exposure          IS [   2 bytes] 9 
 0018,1160 *                           Filter Type          SH [  12 bytes] BODY FILTER 
 0018,1170 *                       Generator Power          IS [   6 bytes] 52800 
 0018,1190 *                         Focal Spot(s)          DS [   8 bytes] 1.200000
 0018,1210 *                    Convolution Kernel          SH [   4 bytes] BONE
 0018,5100 *                      Patient Postiton          CS [   4 bytes] FFS 
 0020,000D *                    Study Instance UID          UI [  36 bytes] 2.16.840.1.113669.16.1.1.706.6428434
 0020,000E *                   Series Instance UID          UI [  54 bytes] 1.2.840.113619.2.80.1943250916.23991.1347374594.1.4.1...
 0020,0010 *                              Study ID          SH [   4 bytes] 5852
 0020,0011 *                         Series Number          IS [   4 bytes] 400 
 0020,0012 *                     Acquistion Number          IS [   2 bytes] 1 
 0020,0013 *                          Image Number          IS [   2 bytes] 9 
 0020,0032 *              Image Position (Patient)          DS [  38 bytes] 12.76631355\-86.25180054\-59.28007507 
 0020,0037 *           Image Orientation (Patient)          DS [  36 bytes] 0.006211060565\0.9999806881\0\0\0\-1
 0020,0052 *                Frame of Reference UID          UI [  58 bytes] 1.2.840.113619.2.278.3.17435652.946.1347312484.524.14515.5...
 0020,1040 *          Position Reference Indicator          LO [   2 bytes] IC
 0020,1041 *                        Slice Location          DS [  12 bytes] 13.29425335 
 0028,0002 *                     Samples per Pixel          US [   2 bytes] 1 [0x0001]
 0028,0004 *            Photometric Interpretation          CS [  12 bytes] MONOCHROME2 
 0028,0010 *                                  Rows       XROWS [   2 bytes] 512 [0x0200]
 0028,0011 *                               Columns    XCOLUMNS [   2 bytes] 512 [0x0200]
 0028,0030 *                         Pixel Spacing          DS [  26 bytes] 0.3320310116\0.3320310116 
 0028,0100 *                        Bits Allocated  XBITSALLOC [   2 bytes] 16 [0x0010]
 0028,0101 *                           Bits Stored          US [   2 bytes] 16 [0x0010]
 0028,0102 *                              High Bit          US [   2 bytes] 15 [0x000f]
 0028,0103 *                  Pixel Representation          US [   2 bytes] 1 [0x0001]
 0028,0120 *                   Pixel Padding Value          US [   2 bytes] 63536 [0xf830]
 0028,1050 *                         Window Center          DS [   4 bytes] 500 
 0028,1051 *                          Window Width          DS [   4 bytes] 2000
 0028,1052 *                     Rescale Intercept          DS [   6 bytes] -1024 
 0028,1053 *                         Rescale Slope          DS [   2 bytes] 1 
 0040,0244 U             General, but not defined.          -- [   8 bytes] 
 0040,0245 U             General, but not defined.          -- [   6 bytes] 
 0040,0253 *           Performed Procedure Step ID          SH [  14 bytes] PPS ID   5852 
 0040,0254 U             General, but not defined.          -- [  22 bytes] 
 7FE0,0010 *                    Pixel (Image) Data  XPIXELDATA [524288 bytes] (data)
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 0008,0008 *                            Image Type          CS [  28 bytes] ORIGINAL\PRIMARY\AXIAL\HELIX
 0008,0012 *                Instance Creation Date          DA [   8 bytes] 20070111
 0008,0013 *                Instance Creation Time          TM [   6 bytes] 165435
 0008,0016 *                         SOP Class UID          UI [  26 bytes] 1.2.840.10008.5.1.4.1.1.2
 0008,0018 *                      SOP Instance UID          UI [  48 bytes] 1.2.840.113704.1.1762580556.1049.1168563275.1685...
 0008,0020 *                            Study Date          DA [   8 bytes] 20070111
 0008,0022 *                      Acquisition Date          DA [   8 bytes] 20070111
 0008,0023 *                            Image Date          DA [   8 bytes] 20070111
 0008,0030 *                            Study Time          TM [   6 bytes] 164517
 0008,0032 *                      Acquisition Time          TM [   6 bytes] 165214
 0008,0033 *                            Image Time          TM [  10 bytes] 165215.047
 0008,0050 *                      Accession Number          SH [   0 bytes] 
 0008,0060 *                              Modality          CS [   2 bytes] CT
 0008,0070 *                          Manufacturer          LO [   8 bytes] Philips 
 0008,0080 *                      Institution Name          LO [   6 bytes] ANNOYN
 0008,0081 *                   Institution Address          ST [   6 bytes] ANNOYN
 0008,0090 *                   Referring Physician          PN [   6 bytes] ANNOYN
 0008,1010 *                          Station Name          SH [   6 bytes] ANNOYN
 0008,1030 *                     Study Description          LO [   6 bytes] ANNOYN
 0008,103E *                    Series Description          LO [   0 bytes] 
 0008,1040 *         Institutional Department Name          LO [  16 bytes] Medical Imaging 
 0008,1070 *                       Operator's Name          PN [   0 bytes] 
 0008,1090 *             Manufacturer's Model Name          LO [   6 bytes] Mx8000
 0008,1140 *                   Ref. Image SEQUENCE          SQ [  98 bytes] <VR type 'SQ': no print format>
 0010,0010 *                        Patient's Name          PN [   6 bytes] ANNOYN
 0010,0020 *                            Patient ID          LO [   6 bytes] ANNOYN
 0010,0030 *                   Patient's Birthdate          DA [   6 bytes] ANNOYN
 0010,0040 *                         Patient's Sex          CS [   6 bytes] ANNOYN
 0010,1010 *                         Patient's Age          AS [   6 bytes] ANNOYN
 0018,0022 *                          Scan Options          CS [   6 bytes] HELIX 
 0018,0050 *                  Slice Thickness (mm)          DS [   4 bytes] 1.3 
 0018,0060 *                        Peak kilovolts          DS [   4 bytes] 140 
 0018,0088 *                Spacing Between Slices          DS [   4 bytes] -1.3
 0018,0090 *              Data Collection Diameter          DS [   4 bytes] 438 
 0018,1020 *                   Software Version(s)          LO [   4 bytes] 2.64
 0018,1030 *                         Protocol Name          LO [   6 bytes] ANNOYN
 0018,1100 *               Reconstruction Diameter          DS [   4 bytes] 438 
 0018,1120 *                  Gantry/Detector Tilt          DS [   2 bytes] 0 
 0018,1130 *                          Table Height          DS [   4 bytes] 125 
 0018,1140 *                    Rotation Detection          CS [   2 bytes] CW
 0018,1151 *                    X-ray Tube Current          IS [   4 bytes] 232 
 0018,1152 *                              Exposure          IS [   4 bytes] 139 
 0018,1160 *                           Filter Type          SH [   2 bytes] B 
 0018,1210 *                    Convolution Kernel          SH [   2 bytes] B 
 0018,5100 *                      Patient Postiton          CS [   4 bytes] HFS 
 0020,000D *                    Study Instance UID          UI [  46 bytes] 1.2.840.113704.1.1762580556.1112.1168562613.11...
 0020,000E *                   Series Instance UID          UI [  46 bytes] 1.2.840.113704.1.1762580556.9014.1168563102.13...
 0020,0010 *                              Study ID          SH [   6 bytes] 19061 
 0020,0011 *                         Series Number          IS [   4 bytes] 5218
 0020,0012 *                     Acquistion Number          IS [   0 bytes] 
 0020,0013 *                          Image Number          IS [   2 bytes] 1 
 0020,0032 *              Image Position (Patient)          DS [  18 bytes] -227\-137\-1378.5 
 0020,0037 *           Image Orientation (Patient)          DS [  12 bytes] 1\0\0\0\1\0 
 0020,0052 *                Frame of Reference UID          UI [  46 bytes] 1.2.840.113704.1.1762580556.9014.1168562971.3...
 0020,0060 *                            Laterality          CS [   0 bytes] 
 0020,1040 *          Position Reference Indicator          LO [   0 bytes] 
 0020,1041 *                        Slice Location          DS [   8 bytes] -1297.5 
 0020,4000 *                        Image Comments          LT [   0 bytes] ~{u~
 0028,0002 *                     Samples per Pixel          US [   2 bytes] 1 [0x0001]
 0028,0004 *            Photometric Interpretation          CS [  12 bytes] MONOCHROME2 
 0028,0010 *                                  Rows       XROWS [   2 bytes] 512 [0x0200]
 0028,0011 *                               Columns    XCOLUMNS [   2 bytes] 512 [0x0200]
 0028,0030 *                         Pixel Spacing          DS [  22 bytes] 0.85546875\0.85546875 
 0028,0100 *                        Bits Allocated  XBITSALLOC [   2 bytes] 16 [0x0010]
 0028,0101 *                           Bits Stored          US [   2 bytes] 12 [0x000c]
 0028,0102 *                              High Bit          US [   2 bytes] 11 [0x000b]
 0028,0103 *                  Pixel Representation          US [   2 bytes] 0 [0x0000]
 0028,1050 *                         Window Center          DS [   8 bytes] 450\450 
 0028,1051 *                          Window Width          DS [  10 bytes] 2000\2000 
 0028,1052 *                     Rescale Intercept          DS [   6 bytes] -1000 
 0028,1053 *                         Rescale Slope          DS [   2 bytes] 1 
 7FE0,0010 *                    Pixel (Image) Data  XPIXELDATA [524288 bytes] (data)


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