[Insight-users] DICOM Image spacing with GDCMImageIO

Sun Jan 18 11:30:47 EST 2009

I'm using GDCMImageIO to read in some 3D dicom data in ITK.  Its a single
file dicom format, so I'm using the reader alone without the series reader.
ITK reads it in with stats:
Input Image Size: [ 384 384 130 ]
Input Image Spacing: [ 0.9375 0.9375 1.88 ]

The size is correct, 384x384 and 130 frames. The spacing, however, I am
concerned about.  Images along both axes requiring inter-frame spacing look
stretched.  I looked in the header (pasted below) and can't find any spacing
information, and certainly no reference to any numbers in [0.9375 0.9375
1.88]. I see:

(0018|0088) Spacing Between Slices = 0.93999999761581

but as I understand it field (0028|0030) should contain pixel spacing, but
it is empty. So, my question is two-fold:

1. Where is ITK getting [ 0.9375 0.9375 1.88 ]?  I am fairly certain this is
incorrect.

2. How can I get the actual spacing of the image to read it in with correct
proportions?

Any help will be greatly appreciated.

      - Aaron

Header:
----------

(0002|0000) Group Length = 200
(0002|0001) File Meta Information Version = AAE=
(0002|0002) Media Storage SOP Class UID = 1.2.840.10008.5.1.4.1.1.4.1
(0002|0003) Media Storage SOP Instance UID =
1.3.46.670589.11.20071.5.20.1.1.8016.2008041212201756468
(0002|0010) Transfer Syntax UID = 1.2.840.10008.1.2.1
(0002|0012) Implementation Class UID = 1.3.46.670589.11.0.0.51.4.4.1
(0002|0013) Implementation Version Name = MR DICOM 4.1
(0008|0005) Specific Character Set = ISO_IR 100
(0008|0008) Image Type = ORIGINAL\PRIMARY\T1\NONE
(0008|0012) Instance Creation Date = 20080412
(0008|0013) Instance Creation Time = 174747
(0008|0014) Instance Creator UID = 1.3.46.670589.11.20071.5
(0008|0016) SOP Class UID = 1.2.840.10008.5.1.4.1.1.4.1
(0008|0018) SOP Instance UID =
1.3.46.670589.11.20071.5.20.1.1.8016.2008041212201756468
(0008|0020) Study Date = 20080412
(0008|0021) Series Date = 20080412
(0008|0023) Content Date = 20080412
(0008|002a) Acquisition Datetime = 20080412122017.53000
(0008|0030) Study Time = 101727
(0008|0031) Series Time = 122017.53000
(0008|0033) Content Time = 174749
(0008|0050) Accession Number = sheep_197
(0008|0060) Modality = MR
(0008|0070) Manufacturer = Philips Medical Systems
(0008|0080) Institution Name = Children's Hospital Boston
(0008|0090) Referring Physician's Name =
(0008|0100) Code Value =
(0008|0102) Coding Scheme Designator = DCM
(0008|0104) Code Meaning =
(0008|1010) Station Name = PHILIPS-58DBFE8
(0008|1030) Study Description = sheep_197
(0008|103e) Series Description = CHILD_3D_bTFE_NAV
(0008|1040) Institutional Department Name = Cardiology
(0008|1070) Operator's Name =
(0008|1080) Admitting Diagnoses Description =
(0008|1090) Manufacturer's Model Name = Achieva
(0008|9123) Creator-Version UID = 1.3.46.670589.11
(0008|9205) Pixel Presentation = MONOCHROME
(0008|9206) Volumetric Properties = VOLUME
(0008|9207) Volume Based Calculation Technique = NONE
(0008|9208) Complex Image Component = MAGNITUDE
(0008|9209) Acquisition Contrast = T1
(0010|0010) Patient's Name = sheep_197
(0010|0020) Patient ID = sheep_197
(0010|0030) Patient's Birth Date = 20070101
(0010|0040) Patient's Sex = O
(0010|1030) Patient's Weight = 38
(0010|21c0) Pregnancy Status = 4
(0018|0015) Body Part Examined = HEART
(0018|0023) MR Acquisition Type = 3D
(0018|0087) Magnetic Field Strength = 1.5
(0018|0088) Spacing Between Slices = 0.93999999761581
(0018|0095) Pixel Bandwidth = 1041.66662597656
(0018|1000) Device Serial Number = 20071
(0018|1020) Software Version(s) = 2.5.3\2.5.3.0
(0018|1030) Protocol Name = CHILD_3D_bTFE_NAV SENSE
(0018|1081) Low R-R Value = 129
(0018|1082) High R-R Value = 1644
(0018|1083) Intervals Acquired = 838
(0018|1084) Intervals Rejected = 0
(0018|5100) Patient Position = FFS
(0018|9004) Content Qualification = PRODUCT
(0018|9005) Pulse Sequence Name = B-TFE
(0018|9008) Echo Pulse Sequence = GRADIENT
(0018|9012) Multi-planar Excitation = NO
(0018|9014) Phase Contrast = NO
(0018|9015) Time of Flight Contrast = NO
(0018|9016) Spoiling = NONE
(0018|9017) Steady State Pulse Sequence = FREE_PRECESSION
(0018|9018) Echo Planar Pulse Sequence = NO
(0018|9020) Magnetization Transfer = NONE
(0018|9021) T2 Preparation = YES
(0018|9022) Blood Signal Nulling = NO
(0018|9024) Saturation Recovery = NO
(0018|9025) Spectrally Selected Suppression = FAT
(0018|9026) Spectrally Selected Excitation = WATER
(0018|9027) Spatial Pre-saturation = NONE
(0018|9028) Tagging = NONE
(0018|9029) Oversampling Phase = 3D
(0018|9032) Geometry of k-Space Traversal = RECTILINEAR
(0018|9033) Segmented k-Space Traversal = PARTIAL
(0018|9034) Rectilinear Phase Encode Reordering = REVERSE_LINEAR
(0018|9035) Tag Thickness =
(0018|9036) Partial Fourier Direction =
(0018|9037) Cardiac Synchronization Technique = PROSPECTIVE
(0018|9051) Transmit Coil Type = BODY
(0018|9053) Chemical Shift Reference = ¸
…ëQ¸@
(0018|9058) MR Acquisition Frequency Encoding Steps = 192
(0018|9059) De-coupling = NO
(0018|9064) k-space Filtering = RIESZ
(0018|9069) Parallel Reduction Factor In-plane =
(0018|9070) Cardiac R-R Interval Specified =
(0018|9073) Acquisition Duration =
(0018|9077) Parallel Acquisition = YES
(0018|9078) Parallel Acquisition Technique = SENSE
(0018|9081) Partial Fourier = NO
(0018|9085) Cardiac Signal Source = VCG
(0018|9090) Velocity Encoding Direction =
(0018|9091) Velocity Encoding Minimum Value =
(0018|9093) Number of k-Space Trajectories = 342
(0018|9094) Coverage of k-Space = ELLIPTICAL
(0018|9100) Resonant Nucleus = 1H
(0018|9101) Frequency Correction = NO
(0018|9155) Parallel Reduction Factor out-of-plane =
(0018|9168) Parallel Reduction Factor Second In-plane =
(0018|9169) Cardiac Beat Rejection Technique = NONE
(0018|9170) Respiratory Motion Compensation Technique = GATING
(0018|9171) Respiratory Signal Source = NAVIGATOR
(0018|9172) Bulk Motion Compensation Technique = NONE
(0018|9174) Applicable Safety Standard Agency = IEC
(0018|9179) Specific Absorption Rate Definition = IEC_WHOLE_BODY
(0018|9180) Gradient Output Type = DB_DT
(0018|9181) Specific Absorption Rate Value =
(0018|9182) Gradient Output = u†'ÆäJ@
(0018|9199) Water Referenced Phase Correction = NO
(0018|9200) MR Spectroscopy Acquisition Type =
(0018|9231) MR Acquisition Phase Encoding Steps in-plane = 192
(0018|9240) RF Echo Train Length = 0
(0018|9241) Gradient Echo Train Length = 12
(0020|000d) Study Instance UID =
1.3.46.670589.11.20071.5.0.5872.2008041210171606230
(0020|000e) Series Instance UID =
1.3.46.670589.11.20071.5.0.8016.2008041212201756468
(0020|0010) Study ID = 261224236
(0020|0011) Series Number = 2201
(0020|0012) Acquisition Number = 22
(0020|0013) Instance Number = 1
(0020|0052) Frame of Reference UID =
1.3.46.670589.11.20071.5.0.5896.2008041211374654004
(0020|1040) Position Reference Indicator =
(0020|9072) Frame Laterality = U
(0028|0002) Samples per Pixel = 1
(0028|0004) Photometric Interpretation = MONOCHROME2
(0028|0008) Number of Frames = 130
(0028|0010) Rows = 384
(0028|0011) Columns = 384
(0028|0100) Bits Allocated = 16
(0028|0101) Bits Stored = 12
(0028|0102) High Bit = 11
(0028|0103) Pixel Representation = 0
(0028|0301) Burned In Annotation = NO
(0028|2110) Lossy Image Compression = 00
(0028|3003) LUT Explanation = Philips Real World Value Mapping
(0028|9001) Data Point Rows = 1
(0028|9002) Data Point Columns = 0
(0040|0241) Performed Station AE Title = PHILIPSMR1
(0040|0244) Performed Procedure Step Start Date = 20080412
(0040|0245) Performed Procedure Step Start Time = 101727
(0040|0250) Performed Procedure Step End Date = 20080412
(0040|0251) Performed Procedure Step End Time = 101727
(0040|0253) Performed Procedure Step ID = 261224236
(0040|0254) Performed Procedure Step Description = sheep_197
(0040|9210) LUT Label = Philips
(2050|0020) Presentation LUT Shape = IDENTITY

-- 
Constantine Aaron Cois, Ph.D.
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