MATLAB Tutorial II Junmo an [email protected] Office Hour: Monday 2:30Pm – 4:30Pm (PGH 315)

MATLAB Tutorial II Junmo an Jman@Cs.Uh.Edu Office Hour: Monday 2:30Pm – 4:30Pm (PGH 315)

MATLAB Tutorial II Junmo An [email protected] Office Hour: Monday 2:30pm – 4:30pm (PGH 315)

Department of Computer Science, University of Houston What is DICOM?

• Digital Imaging and COmmunications in Medicine (DICOM) • A joint project (ACR-NEMA) – The American College of Radiology (ACR) – The National Electrical Manufacturers Association (NEMA) • Reference data and presentations – http://dicom.nema.org/ – ftp://medical.nema.org/medical/Dicom/Multifra me/

2 General Communication Model

DICOM is a vast set of standards Concentrate here on file format for MRI

3 Simplified DICOM File Structure

Metadata Pixel Value

PatientName StudyDate Modality ImageOrientationPatient Public Fields ImagePositionPatient PixelSpacing

…

PrivateFields Private Fields

4 DICOM Terms: Module

Patient Module Attribute Tag Type Attribute Description Patient Name (0010,0010) 2 Patient’s Full Name Patient ID (0010,0020) 2 Primary hospital identification number or code for the patient Issuer of Patient ID (0010,0021) 3 Identifier of the Assigning Authority that issued the Patient ID … (See DICOM Part 3: Information Object Definitions)

• Module: an architectural convenience; a logical group of attributes about a common topic • Type: (1) Required (2) May Be Empty if Unknown (3) Optional (C) Conditional

5 Image Plane Module Attributes

Attribute Tag Type Attribute Description Pixel Spacing (0028,0030) 1 Physical distance in the patient between the center of each pixel, specified by a numeric pair - adjacent row spacing (delimiter) adjacent column spacing in mm. (Pixel Spacing = Row Spacing \ Colum Spacing = 0.30\0.25) Image Orientation (0020,0037) 1 The direction cosines of the first row (Patient) and the first column with respect to the patient. Image Position (Patient) (0020,0032) 1 The x, y, and z coordinates of the upper left hand corner (center of the first voxel transmitted) of the image, in mm. Slice Thickness (0018,0050) 2 Nominal slice thickness, in mm. Slice Location (0020,1041) 3 Relative position of exposure expressed in mm.

6 Geometry Information in DICOM

• DICOM uses a right handed LPH (=LPS) coordinate system. • Relates to patient, not scanner. • DICOM provides public fields that relate a 2D image to 3D patient space. – ImagePositionPatient • Coordinate of top left image pixel. – ImageOrientationPatient • Unit vector along an image row, the unit vector along a column.

Sagittal Transverse Coronal (frontal)

8 ImagePositionPatient (0020,0032)

ImagePositionPatient (x\y\z) ImagePositionPatient -10\-10\5 IPP + origin PixelSpacing 2\4 3 * PixelSpacing[1] 2\-10\5 x-axis

PixelSpacing[0]

y - axis

IPP + 3 * PixelSpacing[0] 2\-6\5

PixelSpacing[1]

• PixelSpacing and Transverse Cut ImagePositionPatient are in mm. • ImageOrientationPatient are two unit vectors (direction cosines). • Height and Width give number of rows IPP = ImagePositionPatient and columns. 9 ImageOrientationPatient (0020,0037)

• Should have 6 values • (Xx\Xy\Xz\Yx\Yy\Yz) – Direction cosines of the image plane relative to the RCS. – The first direction (X vector) is the direction of the image rows in the RCS. – The second direction (Y vector) is the direction of the image columns in the RCS.

RCS = Reference Coordinate System

10 ImageOrientationPatient (0020,0037)

ImagePositionPatient 0\0\10 • 1\0\0\0\1\0 PixelSpacing 1\1

– The X vector is (1,0,0) Z

meaning it is exactly (0,0,10) A X 1\0\0 directed with the image pixel matrix row direction. • (푐표푠 0° , 푐표푠 90° , 푐표푠 90°) – The Y vector is (0,1,0) R L meaning it is exactly directed with the image pixel matrix column Y 0\1\0 P (3,3,10) direction. • (푐표푠 90° , 푐표푠 0° , 푐표푠 90°)

11 ImageOrientationPatient (0020,0037)

• 0.5\0\-0.8660254\0\1\0 – The X vector (0.5,0,-0.8660254) is the direction of the image rows in Z the RCS. • The image rows are rotated 60° from Y the patient's X direction (right-to-left) R and 150° from the patient's Z direction ퟏퟓퟎ° P (feet-to-head). – (푐표푠 60°, 푐표푠 90°, 푐표푠 150°) X ퟔퟎ° – The Y vector (0,1,0) is the direction A

of the image columns in the RCS. L • The patient's Y direction is perpendicular to the image X axis. X 0.5,0,-0.8660254

12 Finding an Image Pixel Coordinate in LPH

IPP + 3 * IOP(1:3) * PixelSpacing[1] + 1* IOP(4:6) * PixelSpacing[0] IPP = ImagePositionPatient IOP = ImageOrientationPatient

13 Putting it all together

• ImageOrientationPatient – rotation • ImagePositionPatient – translation • PixelSpacing – scaling

14 Composing the overall transform

IPP = ImagePositionPatient

15 Direction Cosines in 3D with Homogeneous Coordinates

16 Displaying a 2D image in 3D using surf(X,Y,Z,img)

17 Reading Metadata from DICOM info = dicominfo('CT-MONO2-16-ankle.dcm');

>> info.Modality

ans = CT

18 Reading Image Data from DICOM

I = dicomread('CT- MONO2-16- ankle.dcm');

OR info = dicominfo('CT- MONO2-16- ankle.dcm'); I = dicomread(info);

19 Viewing Images from DICOM Files imshow(I); imshow(I,'DisplayRange colorbar; ',[]); colorbar; – Autoscaling syntax

20 Writing Image Data or Metadata to a DICOM File dicomwrite(I,'ankle.dcm'); Imodified = I; Imodified(Imodified == 4080) = 32; imshow(Imodified,[]);

Removing text characters

21 Shepp-Logan Head Phantom

P = phantom('Modified Shepp- Logan',200); imshow(P);

• 3D Shepp-Logan head phantom – http://www.mathworks.com/matla bcentral/fileexchange/9416 – http://tomography.o-x- t.com/2008/04/13/3d-shepplogan-phantom/ – https://sites.google.com/site/hisp eedpackets/Home/shepplogan

22 Displaying Images of MRI Data load mri; D = squeeze(D); % a 128-by-128-by-1-by-27 array to a 128-by-128-by-27 figure('Colormap',map); image_num = 15; % 1 to 27 image(D(:,:,image_num));

23 Displaying a 2D Contour Slice cm = brighten(jet(length(map)),-.5); figure('Colormap',cm); contourslice(D,[],[],image_num); axis ij; xlim(x); ylim(y); daspect([1,1,1]);

24 Displaying 3D Contour Slices phandles = contourslice(D,[],[],[1,12,19,27],8); view(3); axis tight; set(phandles,'LineWidth',2);

25 Displaying 3D MRI Slices load mri; D = squeeze(D); h=slice(double(D),[],[],1:27); shading interp; colormap gray; alpha(.1);

26 User Driven Orthogonal Slicer

27 Applying an Isosurface to the MRI Data figure('Colormap',map) Ds = smooth3(D); hiso = patch(isosurface(Ds,5),... 'FaceColor',[1,.75,.65],... 'EdgeColor','none'); isonormals(Ds,hiso); view(35,30); hcap = patch(isocaps(D,5),... 'FaceColor','interp',... 'EdgeColor','none'); axis tight; daspect([1,1,.4]); lightangle(45,30); set(gcf,'Renderer','zbuffer'); lighting phong; set(hcap,'AmbientStrength',.6); set(hiso,'SpecularColorReflectance',0,'S pecularExponent',50); 28 User Driven isosurface Plotting

29 Display multiple image frames as rectangular montage load mri; montage(D,map); figure; montage(D, map, 'Indices', 1:9);

30 Managing DICOM Files

• Problem: Thousands of files with meaningless names. How do you store, browse and retrieve the ones you want? • Tools – OsiriX: Mac based viewer. – 3DSlicer: Viewer (Windows, Mac OS X & Linux). – MicroDicom: Viewer working under Windows. – DCM4CHE: Database and web viewer. – Many others – see http://www.idoimaging.com

31 OsiriX

• Free. • Mac based only. • Good functionality. • Popular with clinicians. • OsiriX MD is $649. • Allows user to add and write plugins. • http://www.osirix- viewer.com

32 3DSlicer • Free. • Working under Windows, Mac OS X and Linux. • Good functionality. – Interactive segmentation. – Volume rendering. – 4D Image Viewer. • Extension Manager for exploring and installing plug-ins. • http://www.slicer.org

33 MicroDicom

• Free. • Fast and Light. • Windows based only. • Limited functionality. • Thumbnails view in Windows explorer on .dcm. • http://www.microdico m.com

34 References

• Book – “MATLAB Graphics and Data Visualization Cookbook” by Nivedita et al. – "MATLAB® 7 3-D Visualization" by The MathWorks • Publication – "The Fourier reconstruction of a head section" by Shepp, L.A. et al. – "Three-Dimensional Analytical Magnetic Resonance Imaging Phantom in the Fourier Domain" by Cheng et al. • Lecture Note – “DICOM Technical Concepts” by Kevin O’Donnell – “DICOM (for MRI images)” by David Atkinson

? Do you have any questions? Junmo An [email protected] http://mrl.cs.uh.edu Thank you