[Insight-users] RE: GDCM image size reading

Li, George (NIH/NCI) ligeorge at mail.nih.gov
Thu May 19 14:29:54 EDT 2005


Mathieu:

I have just built the DicomImageReadPrintTags example and run it 
against the dicom image file. Unfortunately, the program crashed, 
complaining the memory could not be "read". In the command line, 
it shows "Meta Group Length 166", which belongs to (0002,0000).
There is no indication where it stopped on the command line.

Anyway, I have attached my own tag printout as an alternative. 
It virtually contains everything needed for interpret the image 
data. For the sake of the confidentiality of patient information, 
I have wiped out the patient personal information. Everything
else are intact.

George


-----Original Message-----
From: Mathieu Malaterre [mailto:mathieu.malaterre at kitware.com] 
Sent: Thursday, May 19, 2005 1:04 PM
To: Li, George (NIH/NCI)
Cc: Miller, James V (Research); insight-users at itk.org
Subject: Re: GDCM image size reading


George,

	Before you send us any images could you simply run:

$ ./bin/DicomImageReadPrintTags image.dcm

And then send us the output of the program.

Thanks
Mathieu

Li, George (NIH/NCI) wrote:
> Mathieu and Jim:
>  
> I recently ran into another problem that maybe related to GDCM.  The 
> problem seems image specific.  The image opened only contains part of 
> the image.  Presumably it has 512x512 pixels in single slice, but only 
> about 2/3 of the image shows.  I looked at the header and there is no 
> values for the "column" and the "row" information that are used to 
> describe the image size.  Therefore, could you tell me how GDCM get 
> the image size information, presumably from other items?
>  
> Interestingly enough, another sets of images from the same scanner 
> without the column and row information are read correctly by GDCM. 
> These phenomena are reproducible.
>  
> I have hard time to locate where is the problem.  Could you help me 
> out here? I can send you a couple of images directly to you for 
> testing purpose upon your response, but please do not use them 
> publically. The images are MRI images from a Philips scanner.
>  
> Thanks,
>  
> George

-------------- next part --------------
File Name =                F:\George's Fusion_042505\ABHYAN_1\MRI\T2\I0001_1
TYPE(tp) DEFINE 0:un, 1:i16, 2:i32, 3:ui16, 4:ui16x2, 5:ui32, 6:f32, 7:d64, 8: seq, 9: str, 10:bData, 11:wData

---=== DICOM Header ===---

Mem   (grp ,elm ) [VR] tp        Info about value field:  len Value field

0084: (0002,0000) [UL]  5                      Group Length:    4 166
0090: (0002,0001) [OB] 10     File Meta Information Version:    2 
009e: (0002,0002) [UI]  9       Media Storage SOP Class UID:   26 1.2.840.10008.5.1.4.1.1.4 
00c0: (0002,0003) [UI]  9    Media Storage SOP Instance UID:   54 1.2.840.113704.7.0.1.137.187.184.7.1113395710453.1002 
00fe: (0002,0010) [UI]  9               Transfer Syntax UID:   20 1.2.840.10008.1.2.1 
011a: (0002,0012) [UI]  9          Implementation Class UID:   20 1.2.840.113704.7.0.2
0136: (0008,0005) [CS]  9            Specific Character Set:   10 ISO_IR 100
0148: (0008,0008) [CS]  9                        Image Type:   26 ORIGINAL\PRIMARY\M_SE\M\SE
016a: (0008,0012) [DA]  9            Instance Creation Date:    8 20040819
017a: (0008,0013) [TM]  9            Instance Creation Time:    6 124829
0188: (0008,0014) [UI]  9              Instance Creator UID:   24 1.3.46.670589.11.5728.5 
01a8: (0008,0016) [UI]  9                     SOP Class UID:   26 1.2.840.10008.5.1.4.1.1.4 
01ca: (0008,0018) [UI]  9                  SOP Instance UID:   54 1.2.840.113704.7.0.1.137.187.184.7.1113395710453.1002 
0208: (0008,0020) [DA]  9                        Study Date:    8 20040819
0218: (0008,0021) [DA]  9                       Series Date:    8 20040819
0228: (0008,0023) [DA]  9                      Content Date:    8 20040819
0238: (0008,0030) [TM]  9                        Study Time:   14 114510.000000 
024e: (0008,0031) [TM]  9                       Series Time:   14 120009.000000 
0264: (0008,0033) [TM]  9                      Content Time:   10 120009.00 
0276: (0008,0050) [SH]  9                  Accession Number:   10 MR0412866 
0288: (0008,0060) [CS]  9                          Modality:    2 MR
0292: (0008,0070) [LO]  9                      Manufacturer:   24 Philips Medical Systems 
02b2: (0008,0080) [LO]  9                  Institution Name:    6 NIH 3T
02c0: (0008,0081) [ST]  9               Institution Address:    0 
02c8: (0008,0090) [PN]  9        Referring Physician's Name:   10 KIM^LYNDON
02da: (0008,1010) [SH]  9                      Station Name:    4 MR4 
02e6: (0008,1030) [LO]  9                 Study Description:   24 MRI BRAIN-Perfusion (IP)
0306: (0008,103e) [LO]  9                Series Description:   16 BRAIN      T2 AX
031e: (0008,1040) [LO]  9     Institutional Department Name:    0 
0326: (0008,1048) [PN]  9            Physician(s) of Record:    0 
032e: (0008,1050) [PN]  9       Performing Physician's Name:    0 
0336: (0008,1060) [PN]  9  Name of Physicians Reading Study:    0 
033e: (0008,1070) [PN]  9                   Operators' Name:    0 
0346: (0008,1080) [LO]  9   Admitting Diagnoses Description:    0 
034e: (0008,1090) [LO]  9         Manufacturer's Model Name:    6 Intera
035c: (0008,1111) [SQ]  0                SQ nested data set:  200 (= sum of all SQ item length)
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0382: (0008,0012) [DA]  8            Instance Creation Date:    8 20040819
0392: (0008,0013) [TM]  8            Instance Creation Time:    6 124840
03a0: (0008,0014) [UI]  8              Instance Creator UID:   24 1.3.46.670589.11.5728.5 
03c0: (0008,1150) [UI]  8          Referenced SOP Class UID:   24 1.2.840.10008.3.1.2.3.3 
03e0: (0008,1155) [UI]  8       Referenced SOP Instance UID:   62 1.3.46.670589.11.0.0.11.4.2.0.5728.5.3048.2004081911450800241 
0426: (0020,0013) [IS]  8                   Instance Number:    2 0 
0426: (0020,0013) [SQ]  8                SQ nested data set:    0 (= end of the SQ item series)
0430: (0008,1140) [SQ]  0                SQ nested data set:  402 (= sum of all SQ item length)
043c: (fffe,e000) [--]  8                SQ nested data set:    0 
0444: (0008,0005) [CS]  8            Specific Character Set:   16 ISO 2022 IR 100 
045c: (0008,1150) [UI]  8          Referenced SOP Class UID:   26 1.2.840.10008.5.1.4.1.1.4 
047e: (0008,1155) [UI]  8       Referenced SOP Instance UID:   60 1.3.46.670589.11.0.0.11.4.2.0.5728.5.872.2004081911593865990
04c2: (fffe,e000) [--]  8                SQ nested data set:    0 
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04e2: (0008,1150) [UI]  8          Referenced SOP Class UID:   26 1.2.840.10008.5.1.4.1.1.4 
0504: (0008,1155) [UI]  8       Referenced SOP Instance UID:   60 1.3.46.670589.11.0.0.11.4.2.0.5728.5.872.2004081911544496964
0548: (fffe,e000) [--]  8                SQ nested data set:    0 
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0568: (0008,1150) [UI]  8          Referenced SOP Class UID:   26 1.2.840.10008.5.1.4.1.1.4 
058a: (0008,1155) [UI]  8       Referenced SOP Instance UID:   60 1.3.46.670589.11.0.0.11.4.2.0.5728.5.872.2004081911550598970
058a: (0008,1155) [SQ]  8                SQ nested data set:    0 (= end of the SQ item series)
05ce: (0010,0010) [PN]  9                    Patient's Name:   32 XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
05f6: (0010,0020) [LO]  9                        Patient ID:    8 XXXXXXX 
0606: (0010,0030) [DA]  9              Patient's Birth Date:    8 XXXXXXXX
0616: (0010,0040) [CS]  9                     Patient's Sex:    2 M 
0620: (0010,1030) [DS]  9                  Patient's Weight:    4 83.0
062c: (0010,2000) [LO]  9                    Medical Alerts:    0 
0634: (0010,2110) [LO]  9                Contrast Allergies:    0 
063c: (0010,2160) [SH]  9                      Ethnic Group:    2 5 
0646: (0010,2180) [SH]  9                        Occupation:    0 
064e: (0010,21b0) [LT]  9        Additional Patient History:    0 
0656: (0010,21c0) [US]  3                  Pregnancy Status:    2 4
0660: (0010,4000) [LT]  9                  Patient Comments:    0 
0668: (0018,0020) [CS]  9                 Scanning Sequence:    2 SE
0672: (0018,0021) [CS]  9                  Sequence Variant:    2 SK
067c: (0018,0022) [CS]  9                      Scan Options:    2 SP
0686: (0018,0023) [CS]  9               MR Acquisition Type:    0 
068e: (0018,0024) [SH]  9                     Sequence Name:    0 
0696: (0018,0050) [DS]  9                   Slice Thickness:    4 5.0 
06a2: (0018,0080) [DS]  9                   Repetition Time:    6 5400.0
06b0: (0018,0081) [DS]  9                         Echo Time:    6 100.0 
06be: (0018,0082) [DS]  9                    Inversion Time:    4 0.0 
06ca: (0018,0083) [DS]  9                Number of Averages:    4 1.0 
06d6: (0018,0084) [DS]  9                 Imaging Frequency:   16 127.789449999999
06ee: (0018,0085) [SH]  9                    Imaged Nucleus:    2 1H
06f8: (0018,0086) [IS]  9                    Echo Number(s):    2 1 
0702: (0018,0087) [DS]  9           Magnetic Field Strength:    4 3.0 
070e: (0018,0088) [DS]  9            Spacing Between Slices:    4 5.0 
071a: (0018,0089) [IS]  9    Number of Phase Encoding Steps:    4 300 
0726: (0018,0091) [IS]  9                 Echo Train Length:    2 15
0730: (0018,0093) [DS]  9                  Percent Sampling:    4 80.0
073c: (0018,0094) [DS]  9       Percent Phase Field of View:    4 75.0
0748: (0018,1000) [LO]  9              Device Serial Number:    6 05728 
0756: (0018,1020) [LO]  9               Software Version(s):   34 NT 10.4.1\PIIM V2.1.4.1 MIMIT MCS 
0780: (0018,1030) [LO]  9                     Protocol Name:    6 T2 AX 
078e: (0018,1081) [IS]  9                     Low R-R Value:    2 0 
0798: (0018,1082) [IS]  9                    High R-R Value:    2 0 
07a2: (0018,1083) [IS]  9                Intervals Acquired:    2 0 
07ac: (0018,1084) [IS]  9                Intervals Rejected:    2 0 
07b6: (0018,1088) [IS]  9                        Heart Rate:    2 0 
07c0: (0018,1100) [DS]  9           Reconstruction Diameter:    6 220.0 
07ce: (0018,1250) [SH]  9                    Receiving Coil:   10 SENSE-head
07e0: (0018,1251) [SH]  9                 Transmitting Coil:    2 B 
07ea: (0018,1310) [US]  3                Acquisition Matrix:    8 0
07fa: (0018,1312) [CS]  9          Phase Encoding Direction:    4 ROW 
0806: (0018,1314) [DS]  9                        Flip Angle:    4 90.0
0812: (0018,5100) [CS]  9                  Patient Position:    4 HFS 
081e: (0020,000d) [UI]  9                Study Instance UID:   52 1.2.124.113532.128.231.96.56.20040819.112059.1221721
085a: (0020,000e) [UI]  9               Series Instance UID:   62 1.3.46.670589.11.0.0.11.4.2.0.5728.5.4780.2004081912000900229 
08a0: (0020,0010) [SH]  9                          Study ID:   10 MR0412866 
08b2: (0020,0011) [IS]  9                     Series Number:    4 401 
08be: (0020,0012) [IS]  9                Acquisition Number:    2 4 
08c8: (0020,0013) [IS]  9                   Instance Number:    2 1 
08d2: (0020,0032) [DS]  9          Image Position (Patient):   50 -113.62694502911\-111.12638258008\-20.798272003115
090c: (0020,0037) [DS]  9       Image Orientation (Patient):  102 0.99836278743125\-0.0193718230561\-0.0538189292347\0.00894695507015\0.98221021046134\-0.1875714649419 
097a: (0020,0052) [UI]  9            Frame of Reference UID:   62 1.3.46.670589.11.0.0.11.4.2.0.5728.5.4780.2004081911535378201 
09c0: (0020,0060) [CS]  9                        Laterality:    0 
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09dc: (0020,1040) [LO]  9      Position Reference Indicator:    0 
09e4: (0020,1041) [DS]  9                    Slice Location:    4 0.0 
09f0: (0020,1208) [IS]  9      # of Study Related Instances:    4 1799
09fc: (0020,4000) [LT]  9                    Image Comments:    0 
0a04: (0028,0002) [US]  3                 Samples per Pixel:    2 1
0a0e: (0028,0004) [CS]  9        Photometric Interpretation:   12 MONOCHROME2 
0a22: (0028,0010) [US]  3                              Rows:    2 
0a2c: (0028,0011) [US]  3                           Columns:    2 
0a36: (0028,0030) [DS]  9                     Pixel Spacing:   20 0.4296875\0.4296875 
0a52: (0028,0034) [IS]  9                Pixel Aspect Ratio:    4 1\1 
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0a7c: (0028,0103) [US]  3              Pixel Representation:    2 
0a86: (0028,1050) [DS]  9                     Window Center:    6 
0a94: (0028,1051) [DS]  9                      Window Width:    6 
0aa2: (0028,2110) [CS]  9           Lossy Image Compression:    2 00
0aac: (0032,000a) [CS]  9                   Study Status ID:   10 SCHEDULED 
0abe: (0032,1000) [DA]  9        Scheduled Study Start Date:    8 20040819
0ace: (0032,1001) [TM]  9        Scheduled Study Start Time:   14 113000.000000 
0ae4: (0032,1032) [PN]  9              Requesting Physician:   14 KIM^LYNDON^^^ 
0afa: (0032,1033) [LO]  9                Requesting Service:    4 OP12
0b06: (0032,1060) [LO]  9   Requested Procedure Description:   24 MRI BRAIN-Perfusion (IP)
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0b3a: (0008,0005) [CS]  8            Specific Character Set:   16 ISO 2022 IR 100 
0b52: (0008,0100) [SH]  8                        Code Value:    0 
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0b5a: (0032,1070) [LO]  9          Requested Contrast Agent:    0 
0b62: (0032,4000) [LT]  9                    Study Comments:   24 MRI BRAIN-Perfusion (IP)
0b82: (0038,0050) [LO]  9                     Special Needs:    0 
0b8a: (0038,0300) [LO]  9          Current Patient Location:    4 OP12
0b96: (0038,0500) [LO]  9                     Patient State:    0 
0b9e: (0040,0241) [AE]  9        Performed Station AE Title:   10 MR4INTERA 
0bb0: (0040,0242) [SH]  9            Performed Station Name:    0 
0bb8: (0040,0243) [SH]  9                Performed Location:    0 
0bc0: (0040,0244) [DA]  9  Performed Procedure Step Start Date:    8 20040819
0bd0: (0040,0245) [TM]  9  Performed Procedure Step Start Time:    6 114510
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0c04: (0040,0252) [UN]  0   Performed Procedure Step Status:    0 
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0c42: (0040,0255) [LO]  9  Performed Procedure Type Descript'n:    0 
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0c76: (0040,0007) [LO]  8  Sche'd Procedure Step Descript'n:   24 MRI BRAIN-Perfusion (IP)
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0ca2: (0040,0009) [SH]  8       Scheduled Procedure Step ID:   10 MR0412866 
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0d64: (0040,2009) [SH]  9          Order Enterer's Location:    0 
0d6c: (0040,2010) [SH]  9       Order Callback Phone Number:    0 
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