<span class="Apple-style-span" style="border-collapse: collapse; ">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:<div>
<br></div><div><div>Input Image Size: [ 384 384 130 ]</div><div>Input Image Spacing: [ 0.9375 0.9375 1.88 ]</div><div><br></div><div>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:</div>
<div><br></div><div>(0018|0088) Spacing Between Slices = 0.93999999761581 <br></div><div><br></div><div>but as I understand it field (0028|0030) should contain pixel spacing, but it is empty. So, my question is two-fold:</div>
<div><br></div><div>1. Where is ITK getting [ 0.9375 0.9375 1.88 ]? I am fairly certain this is incorrect.</div><div><br></div><div>2. How can I get the actual spacing of the image to read it in with correct proportions?</div>
<div><br></div><div>Any help will be greatly appreciated.</div><div><br></div><div> - Aaron</div><div><br></div><div><br></div><div><br></div><div><br></div><div>Header:</div><div>----------</div><div><br></div><div>
<div>(0002|0000) Group Length = 200</div><div>(0002|0001) File Meta Information Version = AAE=</div><div>(0002|0002) Media Storage SOP Class UID = 1.2.840.10008.5.1.4.1.1.4.1</div><div>(0002|0003) Media Storage SOP Instance UID = 1.3.46.670589.11.20071.5.20.1.1.8016.2008041212201756468</div>
<div>(0002|0010) Transfer Syntax UID = 1.2.840.10008.1.2.1</div><div>(0002|0012) Implementation Class UID = 1.3.46.670589.11.0.0.51.4.4.1</div><div>(0002|0013) Implementation Version Name = MR DICOM 4.1</div><div>(0008|0005) Specific Character Set = ISO_IR 100</div>
<div>(0008|0008) Image Type = ORIGINAL\PRIMARY\T1\NONE</div><div>(0008|0012) Instance Creation Date = 20080412</div><div>(0008|0013) Instance Creation Time = 174747</div><div>(0008|0014) Instance Creator UID = 1.3.46.670589.11.20071.5</div>
<div>(0008|0016) SOP Class UID = 1.2.840.10008.5.1.4.1.1.4.1</div><div>(0008|0018) SOP Instance UID = 1.3.46.670589.11.20071.5.20.1.1.8016.2008041212201756468</div><div>(0008|0020) Study Date = 20080412</div><div>(0008|0021) Series Date = 20080412</div>
<div>(0008|0023) Content Date = 20080412</div><div>(0008|002a) Acquisition Datetime = 20080412122017.53000</div><div>(0008|0030) Study Time = 101727</div><div>(0008|0031) Series Time = 122017.53000</div><div>(0008|0033) Content Time = 174749</div>
<div>(0008|0050) Accession Number = sheep_197 </div><div>(0008|0060) Modality = MR</div><div>(0008|0070) Manufacturer = Philips Medical Systems </div><div>(0008|0080) Institution Name = Children's Hospital Boston</div>
<div>(0008|0090) Referring Physician's Name = </div><div>(0008|0100) Code Value = </div><div>(0008|0102) Coding Scheme Designator = DCM </div><div>(0008|0104) Code Meaning = </div><div>(0008|1010) Station Name = PHILIPS-58DBFE8 </div>
<div>(0008|1030) Study Description = sheep_197 </div><div>(0008|103e) Series Description = CHILD_3D_bTFE_NAV </div><div>(0008|1040) Institutional Department Name = Cardiology</div><div>(0008|1070) Operator's Name = </div>
<div>(0008|1080) Admitting Diagnoses Description = </div><div>(0008|1090) Manufacturer's Model Name = Achieva </div><div>(0008|9123) Creator-Version UID = 1.3.46.670589.11</div><div>(0008|9205) Pixel Presentation = MONOCHROME</div>
<div>(0008|9206) Volumetric Properties = VOLUME</div><div>(0008|9207) Volume Based Calculation Technique = NONE</div><div>(0008|9208) Complex Image Component = MAGNITUDE </div><div>(0008|9209) Acquisition Contrast = T1</div>
<div>(0010|0010) Patient's Name = sheep_197 </div><div>(0010|0020) Patient ID = sheep_197 </div><div>(0010|0030) Patient's Birth Date = 20070101</div><div>(0010|0040) Patient's Sex = O </div><div>(0010|1030) Patient's Weight = 38</div>
<div>(0010|21c0) Pregnancy Status = 4</div><div>(0018|0015) Body Part Examined = HEART </div><div>(0018|0023) MR Acquisition Type = 3D</div><div>(0018|0087) Magnetic Field Strength = 1.5 </div><div>(0018|0088) Spacing Between Slices = 0.93999999761581</div>
<div>(0018|0095) Pixel Bandwidth = 1041.66662597656</div><div>(0018|1000) Device Serial Number = 20071 </div><div>(0018|1020) Software Version(s) = 2.5.3\2.5.3.0 </div><div>(0018|1030) Protocol Name = CHILD_3D_bTFE_NAV SENSE </div>
<div>(0018|1081) Low R-R Value = 129 </div><div>(0018|1082) High R-R Value = 1644</div><div>(0018|1083) Intervals Acquired = 838 </div><div>(0018|1084) Intervals Rejected = 0 </div><div>(0018|5100) Patient Position = FFS </div>
<div>(0018|9004) Content Qualification = PRODUCT </div><div>(0018|9005) Pulse Sequence Name = B-TFE </div><div>(0018|9008) Echo Pulse Sequence = GRADIENT</div><div>(0018|9012) Multi-planar Excitation = NO</div><div>(0018|9014) Phase Contrast = NO</div>
<div>(0018|9015) Time of Flight Contrast = NO</div><div>(0018|9016) Spoiling = NONE</div><div>(0018|9017) Steady State Pulse Sequence = FREE_PRECESSION </div><div>(0018|9018) Echo Planar Pulse Sequence = NO</div><div>(0018|9020) Magnetization Transfer = NONE</div>
<div>(0018|9021) T2 Preparation = YES </div><div>(0018|9022) Blood Signal Nulling = NO</div><div>(0018|9024) Saturation Recovery = NO</div><div>(0018|9025) Spectrally Selected Suppression = FAT </div><div>(0018|9026) Spectrally Selected Excitation = WATER </div>
<div>(0018|9027) Spatial Pre-saturation = NONE</div><div>(0018|9028) Tagging = NONE</div><div>(0018|9029) Oversampling Phase = 3D</div><div>(0018|9032) Geometry of k-Space Traversal = RECTILINEAR </div><div>(0018|9033) Segmented k-Space Traversal = PARTIAL </div>
<div>(0018|9034) Rectilinear Phase Encode Reordering = REVERSE_LINEAR</div><div>(0018|9035) Tag Thickness = </div><div>(0018|9036) Partial Fourier Direction = </div><div>(0018|9037) Cardiac Synchronization Technique = PROSPECTIVE </div>
<div>(0018|9051) Transmit Coil Type = BODY</div><div>(0018|9053) Chemical Shift Reference = ¸ …ëQ¸@</div><div>(0018|9058) MR Acquisition Frequency Encoding Steps = 192</div><div>(0018|9059) De-coupling = NO</div><div>(0018|9064) k-space Filtering = RIESZ </div>
<div>(0018|9069) Parallel Reduction Factor In-plane = </div><div>(0018|9070) Cardiac R-R Interval Specified = </div><div>(0018|9073) Acquisition Duration = </div><div>(0018|9077) Parallel Acquisition = YES </div><div>(0018|9078) Parallel Acquisition Technique = SENSE </div>
<div>(0018|9081) Partial Fourier = NO</div><div>(0018|9085) Cardiac Signal Source = VCG </div><div>(0018|9090) Velocity Encoding Direction = </div><div>(0018|9091) Velocity Encoding Minimum Value = </div><div>(0018|9093) Number of k-Space Trajectories = 342</div>
<div>(0018|9094) Coverage of k-Space = ELLIPTICAL</div><div>(0018|9100) Resonant Nucleus = 1H</div><div>(0018|9101) Frequency Correction = NO</div><div>(0018|9155) Parallel Reduction Factor out-of-plane = </div><div>(0018|9168) Parallel Reduction Factor Second In-plane = </div>
<div>(0018|9169) Cardiac Beat Rejection Technique = NONE</div><div>(0018|9170) Respiratory Motion Compensation Technique = GATING</div><div>(0018|9171) Respiratory Signal Source = NAVIGATOR </div><div>(0018|9172) Bulk Motion Compensation Technique = NONE</div>
<div>(0018|9174) Applicable Safety Standard Agency = IEC </div><div>(0018|9179) Specific Absorption Rate Definition = IEC_WHOLE_BODY</div><div>(0018|9180) Gradient Output Type = DB_DT </div><div>(0018|9181) Specific Absorption Rate Value = </div>
<div>(0018|9182) Gradient Output = u†'ÆäJ@</div><div>(0018|9199) Water Referenced Phase Correction = NO</div><div>(0018|9200) MR Spectroscopy Acquisition Type = </div><div>(0018|9231) MR Acquisition Phase Encoding Steps in-plane = 192</div>
<div>(0018|9240) RF Echo Train Length = 0</div><div>(0018|9241) Gradient Echo Train Length = 12</div><div>(0020|000d) Study Instance UID = 1.3.46.670589.11.20071.5.0.5872.2008041210171606230</div><div>(0020|000e) Series Instance UID = 1.3.46.670589.11.20071.5.0.8016.2008041212201756468</div>
<div>(0020|0010) Study ID = 261224236 </div><div>(0020|0011) Series Number = 2201</div><div>(0020|0012) Acquisition Number = 22</div><div>(0020|0013) Instance Number = 1 </div><div>(0020|0052) Frame of Reference UID = 1.3.46.670589.11.20071.5.0.5896.2008041211374654004</div>
<div>(0020|1040) Position Reference Indicator = </div><div>(0020|9072) Frame Laterality = U </div><div>(0028|0002) Samples per Pixel = 1</div><div>(0028|0004) Photometric Interpretation = MONOCHROME2 </div><div>(0028|0008) Number of Frames = 130 </div>
<div>(0028|0010) Rows = 384</div><div>(0028|0011) Columns = 384</div><div>(0028|0100) Bits Allocated = 16</div><div>(0028|0101) Bits Stored = 12</div><div>(0028|0102) High Bit = 11</div><div>(0028|0103) Pixel Representation = 0</div>
<div>(0028|0301) Burned In Annotation = NO</div><div>(0028|2110) Lossy Image Compression = 00</div><div>(0028|3003) LUT Explanation = Philips Real World Value Mapping</div><div>(0028|9001) Data Point Rows = 1</div><div>(0028|9002) Data Point Columns = 0</div>
<div>(0040|0241) Performed Station AE Title = PHILIPSMR1</div><div>(0040|0244) Performed Procedure Step Start Date = 20080412</div><div>(0040|0245) Performed Procedure Step Start Time = 101727</div><div>(0040|0250) Performed Procedure Step End Date = 20080412</div>
<div>(0040|0251) Performed Procedure Step End Time = 101727</div><div>(0040|0253) Performed Procedure Step ID = 261224236 </div><div>(0040|0254) Performed Procedure Step Description = sheep_197 </div><div>(0040|9210) LUT Label = Philips </div>
<div>(2050|0020) Presentation LUT Shape = IDENTITY</div><div><br></div></div></div></span>-- <br>Constantine Aaron Cois, Ph.D.<br>