Outline 6.1 MR Image Formation Matrix, Gradients & Signals Image formation & k-pace • Imaging Matrix • Gradients & Signals • Phase, Frequency and Amplitude • Slice selection • Phase encoding • Frequency encoding Carolyn Kaut Roth, RT (R)(MR)(CT)(M)(CV) FSMRT CEO Imaging Education Associates candi@imaginged.com www.imaginged.com Slide # 2 Objectives Imaging Matrix Upon completion of this course, the attendee should… 1. Learn about the matrix. 2. Understand the MR signals and how they are affected by gradients 3. Learn the concept phase, frequency & amplitude. 4. Understand image formation, slice selection, phase encoding, frequency encoding 5. Understand the concept of k-space. • Digital images are created with a matrix • Smallest unit of the digital image is a pixel 3x3 6x6 Slide # 3 Slide # 4 Pixel , Voxel What makes up a digital image? • In MRI slices are acquired • The voxel is a 3d volume element •The face of the voxel is the pixel Voxel Slice Thickness • The size of the area imaged in MRI is the field of view (FOV) • The number of pixels (rows x columns) is the matrix • The depth is the slice thickness matrix matrix Pixel Slide # 5 Slice Thickness FOV Slice Thickness FOV Slide # 6 1 Calculating pixel size Calculating pixel & voxel size • Isotropic voxel • to calculate the pixel size • to calculate the voxel size FOV FOV = = Thickness Matrix Matrix equals matrix FOV Voxel equals • Pixel size FOV x Matrix FOV Matrix by FOV Matrix Pixel • Area of the Pixel (mm2) FOV Matrix Slice Thickness Pixel Slice Thickness FOV x Matrix times FOV Matrix • Voxel Volume (mm3) FOV x Matrix FOV Matrix FOV Matrix Slice Thickness times Voxel FOV x Thickness Matrix times Slide # 7 Slide # 8 Pixel Size and FOV Pixel Size and Matrix • higher matrix • smaller pixel • less tissue in the pixel • higher resolution • smaller FOV • smaller pixel • less tissue in the pixel • higher resolution 3x3 6x6 Pixel Larger FOV Smaller FOV Pixel Pixel Slide # 9 Pixel Slide # 10 Pixel Size and Slice thickness Imaging Planes • smaller thickness • smaller pixel • less tissue in the pixel • higher resolution • What Views (Planes) Smaller thickness Larger thickness – Sagittal – Axial – Coronal – Oblique Sagittal •What Contrast (Planes) Pixel Pixel Slide # 11 – TR – TE Axial Slide # 12 Coronal 2 Timing Diagrams – RF & Gradient Pulses To Create MR Images TR (Repetition Time) TR, is the time between 900 RF pulses • The patient is placed in the magnetic field RF Pulse Slice selection gradient –to align the spins Phase Encoding gradient These lines represent gradient pulses • The RF pulse is applied –to excite the spins –at the Larmor Frequency Frequency encoding gradient MR signal induced in the receiver coil MR signal TE (Echo Time) Slide # 13 Slide # 14 Short & Long TR Imaging MR Excitation Relaxation Short TR Bo 1800 900 RF Pulse Z Z Z Mz 900 Mxy X X MR Signal FID Long TR 1800 Y Y Alignment RF Receiver coil Excitation 900 Relaxation Slide # 15 Slide # 16 Timing Diagram Timing Diagram -TE TR (Repetition Time) 1800 1800 900 Proton density-TE1 T2WI-TE2 T2 decay TE (Echo Time) FID echo TE 1 Image with artifact Slide # 17 echo TE 2 Cleaned up the “SIC” Slide # 18 3 Imaging Planes Imaging Planes • What Views (Planes) – Sagittal – Axial – Coronal – Oblique Sagittal •What Contrast (Planes) – TR – TE Axial Sagittal Slide # 19 Coronal Slice selection gradient Phase Encoding gradient PE (Y) FE (X) Oblique Slice Selection • If the magnetic field is homogeneous, the frequency is the same … head to feet • If the RF is applied… in this case the entire body would be excited RF Pulse SS (Z) Axial (Transverse) Slide # 20 Timing Diagram – Gradients- logical coordinate system Gradients Coronal Frequency encoding gradient MR signal Slide # 21 Homogeneous magnetic field The frequency is the same from the head to the feet Slide # 22 Selecting an Axial Slice – Physical Coordinate System Selective Excitation •To excite a location within the imager, within the body.. • A magnetic field gradient is applied • The RF pulse is applied that matches a location Homogeneous magnetic field gradient Axial slice Z gradient Superior to Inferior Slide # 23 Homogeneous magnetic field With a linear gradient field applied Slide # 24 4 Selecting a Coronal Slice - Physical Coordinate System Selecting a Sagittal Slice - Physical Coordinate System X gradient Right to Left Y gradient Anterior to Posterior Coronal slice Sagittal slice Slide # 25 Slide # 26 Phase & Frequency Encoding Outline Gradient S to I • Once the slice is selected… • Encoding along the other axes, –With gradients •R to L •A to P Axial slice selection Gradient R to L • Imaging Matrix • Gradients & Signals • Phase, Frequency and Amplitude • Slice selection • Phase encoding • Frequency encoding Gradient A to P –For encoding •Phase encoding •Frequency encoding Axial slice Slide # 27 Periodic signals Slide # 28 Amplitude wavelength Low Amplitude Signal Phase Frequency Medium Amplitude Signal Amplitude Wavelength Enhanced Brain Image High Amplitude Signal Slide # 29 Slide # 30 5 Frequency Phase 1 second Periodic signal Sine wave Frequency = # times it repeats in a period of time cycles per second or Hertz (Hz) or million cycles per second , or megahertz (MHz) What phase of the precession where along the precessional path In phase Out of phase 1 cycles per second Revolutions along the precessional path In Phase Out of phase 2 cycles per second 4 cycles per second Slide # 31 Slide # 32 Phase & Frequency Phases of Periodic Signals 90 degrees 0 degrees 180 degrees 360 degrees 0 degrees 90 degrees 180 degrees 270 degrees 270 degrees Frequency is the rate of precession Phase is a positionSlide along a precessional path # 33 Changing the Frequency and Phase Steep Gradient High Amplitude Gradient High changes in frequencies Big changes in phase De phased Low signal Low amplitude signal Low Gradient Low Amplitude Gradient Small changes in frequencies Small changes in phase In phase High signal High amplitude signal Slide # 35 Slide # 34 Signal Amplitude Phase & Frequency = Where Amplitude = What color Black – Low Amplitude Gray – Medium Amplitude White – High amplitude Slide # 36 6 Phase & Frequency K-Space & MR Imaging Phase & Frequency = Where Same frequency – different phase Amplitude = What color Black, low K-space (raw signal data) Gray, med White, high amplitude signal Phase & Frequency = Where Phase lines in k-space Freqency – points along each line Same phase different frequency Same phase and frequency, different ampltude Slide # 37 MR Image) Slide # 38 CT Image Acquisition Back Projection Phantom X-ray Xray Water Projection Detectors Water Projection In CT, the xray tube rotates around the “phantom” In this case the x-ray beam is attenuated by the water in the phantom, and therfore “projects” a “shadow” within the detectors… Slide # 39 Slide # 40 Back Projection - Reconstruction MR Image Formation • In order to define a point in space, we need three coordintes X, Y & Z Where the lines intersect, there could be water in the phantom Two projections are not enough! Projection #1 Projection #3 He third projection allowed for the image! Projection #2 Slide # 41 • To define these three coordinates, we do 3 jobs - slice selection - phase encoding - frequency encoding 3 x 3 Matrix Slide # 42 7 Timing Diagram - Logical Coordinate System Outline • Imaging Matrix • Gradients & Signals • Phase, Frequency and Amplitude • Slice selection • Phase encoding • Frequency encoding RF Pulse Gradients SS (Z) Slice selection gradient Phase Encoding gradient PE (Y) FE (X) Frequency encoding gradient MR signal Slide # 43 Slide # 44 Slice Selection Selective Excitation • If the magnetic field is homogeneous, the frequency is the same … head to feet • If the RF is applied… in this case the entire body would be excited Homogeneous magnetic field The frequency is the same from the head to the feet Slide # 45 •To excite a location within the imager, within the body.. • A magnetic field gradient is applied • The RF pulse is applied that matches a location Slide # 46 Homogeneous magnetic field gradient Homogeneous magnetic field With a linear gradient field applied Slice Thickness & Transmitter Bandwidth Slice Thickness & Gradient Amplitude •If only one frequency is “sent in” or transmitted for excitation, we get a slice as thin as tissue paper. •Steep Gradients (high amplitude) slice selection gradient, produce thin slices. With a given BW, a steep gradient produces a thinner slice This radiofrequency matches the location in the mid section of this patient, hence a thin axial slice in the belly •For a thicker slice a range of frequencies is “transmitted” known as the Transmit Bandwidth FYI… This is not the bandwidth that we typically “set” during image acquisition. That is the receiver bandwidth. Receive bandwidth will be discussed later in this section This range of radiofrequencies (or Bandwidth) matches the location 47this patient, hence a thin axial slice in the belly in the mid Slide section# of •Flatter Gradients (low amplitude) slice selection gradient, produce thicker slices. •“Steep things make skinny things!” With a given BW, a flatter gradient produces a thicker slice Slide # 48 8 Imaging Planes & Slice Selection Gradients Physical vs Logical Gradients Logical Gradients RF pulses for spin echo Z gradient Physical Gradients •Slice Selection Z (runs superior to inferior) (axial) Y (A-P) (coronal) X (R-L) (sagittal) Z Slice Selection Axial slice Z gradient Superior to Inferior Sagittal slice X gradient Right to Left •Phase Encoding -Depends upon the plane smaller word smaller anatomy (motion) smaller matrix (time) Y Phase Encoding X Frequency Encoding Phase Phase •Frequency Encoding -Depends upon the plane Frequency Z & Y gradient Anterior to Posterior Slide # 49 Frequency The gradient used for oblique depend upon the oblique desired Coronal slice Y gradient Anterior to Posterior motion Slide # 50 Spatial Encoding within the Slice Spatial Encoding within the Slice Gradient S to I • Once the slice is selected • Encoding along the other axes, –With gradients Axial slice selection •R to L •A to P Gradient A to P –For encoding •Phase encoding •Frequency encoding Gradient R to L Fourier states that any “shape” can be reconstructed by periodic signals Slide # 51 Slide # 52 Fourier Transformation – Step #1 Fourier Transformation – Step #2 Step #2 •Let’s take another sine wave with lower amplitude and higher frequency •And try again Step #1 •Let’s take one sine wave and •Try to produce a “ramp” Sine wave Ramp Sine wave •Not Even close… Ramp •Better… Step #1 Storage space K-space Slide # 53 ? Image Storage space K-space ? Image Slide # 54 9 Fourier Transformation – Step #3 Fourier Transformation – step #4 Step #3 •Let’s take another sine wave with lower amplitude and higher frequency •And try again Sine wave Ramp Step #4 •Let’s take another sine wave with lower amplitude and higher frequency •And try again Sine wave Ramp •Better but no cigar! The Ramp Storage space K-space •Not Bad! ? Image The Ramp Storage space Slide # 55 K-space ? Image Slide # 56 Truncation Artifact – 2D Fourier Tranform (2DFT) K-space - Sampling Center of K-space for Contrast Signal to Noise Edges of K-space Detail Resolution K-space Brain image 128 phase matrix Brain image 256 phase matrix Image Matrix Edge Center Virtually no visible truncation Artifact Truncation Artifact Less Samples Edge More Samples Storage space Slide # 57 Image Formation & K-space filling K-space for Mona Lisa All lines filled Image Slide # 58 Image Formation & K-space filling K-space for Mona Lisa Edges Filled Slide # 59 K-space Resolution But no contrast… Slide # 60 10 Fourier Transformation Image Formation & K-space filling Ft K-space for Mona Lisa Center lines filled Contrast but No resolution… K-space for Mona Lisa All lines filled Fourier transformer will do FT, one at a time Array processor will to an “array” of FT’s Slide # 61 Slide # 62 Let’s Make an MR Image… Outline Gradient S to I • Select a slice • Encode along the other axes, –With gradients Axial slice selection •R to L •A to P Gradient A to P –Encoding Steps • Imaging Matrix • Gradients & Signals • Phase, Frequency and Amplitude • Slice selection • Phase encoding • Frequency encoding •Phase encoding •Frequency encoding Gradient R to L Slide # 63 Slide # 64 Image Acquisition & Image Formation Sampling MR Signal • Signals are created by a 900 and a 1800 pulse • Signals are sampled during “readout” at TE • Points are “stored” in k-space for until enough points are sampled to create an MR Image RF SS (Z) Phase matrix & FOV PE (Y) K-space sampling points K-space sampling points signals in K-space Readout Frequency Encoding Gradient Frequency matrix & FOV FE (X) Signal Signal Timing Diagram K-space Not the image (raw data) Slide # 65 Image matrix (# phase & # frequency steps) TE Slide # 66 11 Nyquist Therum Aliasing • Signals must be samples at least twice per cycle • This means that they must be sampled at the highest frequency • Sampling is performed at a given time interval (t) based on the frequency t Signals sampled at a given time interval • If signals are not sampled at the appropriate time interval • Signals are not sampled properly • This results in aliasing t Signals sampled at a given time interval Aliasing Signals reproduced from sampling points Undersampled signals, reproduce the wrong frequency Signals reproduced from sampling points Slide # 67 Undersampled signals Slide # 68 K-Space K-Space • K-space has lines, # Phase encoding steps • And points along each line, # Frequency steps •Steep (-) phase encoding gradient •Sample the echo •“Store” in k-space Steep negative gradient Phase Phase matrix & FOV Steep negative gradient Phase Frequency matrix & FOV Frequency Sample points along the echo Slide # 69 Frequency Points stored in the bottom line of k-space Slide # 70 Image Formation K-Space • Less Steep (-) phase encoding gradient •Sample the echo •“Store” in k-space Less Steep negative gradient Phase Less Steep negative gradient Steep negative gradient Sample points along the echo Slide # 71 Frequency Points stored in the bottom of k-space Edges only Center only Slide # 72 12 Image Formation Image Formation •Less Steep (-) phase encoding gradient •Sample the echo •“Store” in k-space Less Steep negative gradient •Flat phase encoding gradient •Sample the echo •“Store” in k-space Flat gradient Flat gradient Less Steep negative gradient Less Steep negative gradient Steep negative gradient Sample points along the echo Phase Phase Less Steep negative gradient Less Steep negative gradient Steep negative gradient Frequency Points stored in the bottom of k-space Sample points along the echo Slide # 73 Frequency Points stored in the middle of k-space Slide # 74 Image Formation Image Formation •Low amp (+) phase encoding gradient •Sample the echo •“Store” in k-space Less Steep positive gradient •Steeper (+) phase encoding gradient •Sample the echo •“Store” in k-space Steeper positive gradient Higher positive amplitude positive Low amplitude positive Flat gradient Less Steep negative gradient Less Steep negative gradient Steep negative gradient Sample points along the echo Phase Phase Low amplitude positive Flat gradient Less Steep negative gradient Less Steep negative gradient Steep negative gradient Frequency Points stored in the top of k-space Slide # 75 Sample points along the echo Frequency Points stored in the top of k-space Slide # 76 Image Formation K-space & Image Formation •Steep (+) phase encoding gradient •Sample the echo •“Store” in k-space Steepest positive gradient Phase Highest positive amplitude positive Higher positive amplitude positive Low amplitude positive Flat gradient Less Steep negative gradient Less Steep negative gradient Steep negative gradient Sample points along the echo Slide # 77 Frequency Points stored in the top line of k-space Scan Time TR x # of Phase Views x NSA Slide # 78 13 Motion Artifact Outline • Imaging Matrix • Gradients & Signals • Phase, Frequency and Amplitude • Slice selection • Phase encoding • Frequency encoding • k-space manipulation Slide # 79 Filling k-space Slide # 80 *Assume 256 phase matrix for this entire module Remember: The amplitude of the phase encoding gradient applied during the FID "encodes" the sampled echo for a particular phase "line" or "profile" in k-space + 128 ky Linear Filling Fills from "bottom" up ky 0 ky + 128 ky 0 ky kx - 128 ky kx These red arrows represent the echoes sampled following a given phase gradient applied during the FID - 128 ky If we desire a final image with 256 pixel resolution in the phase direction of our FOV, then we will need to acquire 256 distinctive lines of acquisition filling the data points in k-space -128, -127, -126....-1, 0, +1, +2 ... +126, +127, +128 Slide # 81 Slide # 82 Centric Filling Elliptic Filling This technique acquires high signal data "lines" first Fills from "Middle" out + 128 ky ky Remember: X = Frequency Y = Phase Z = Slice ky 0 ky Often used in Contrast Enhanced MRA studies kx - 128 ky This technique acquires the most "central" data points first Fills from "Center" out + 128 ky ky *The center data points in k-space contribute 0 ky most to the final images signal (contrast) 3D acquisition used for Contrast Enhanced MRA to minimize venous filling kz - 128 ky 0, +1, -1, +2, -2, +3, -3..............+128, -128 Slide # 83 These techniques fill k-space in either a "symmetrical" fashion as shown here, or in a random pattern from the center data points outward Slide # 84 14 Number of Signals Averaged (NSA) Reducing NSA Scan Time = TR x Ny x NSA Scan Time = TR x Ny x NSA + 128 ky 1 NSA 1 NSA ky Reducing NSA 2 NSA 0 ky 3 NSA - 128 ky 2 NSA Reduces scan time DOES NOT reduce spatial resolution Increases noise (reduces SNR) Increased flow/motion artifacts 4 NSA Think of the NSA as "coats of paint" It's the number of times each "line" or "phase view" of k-space is sampled Image courtesy Dr. Val Runge 4 NSA Image courtesy Dr. Val Runge Slide # 85 Slide # 86 Partial Fourier Reducing Phase Matrix Scan Time = TR x Ny x NSA Scan Time = TR x Ny x NSA Ky 3 NSA Ky +y Interpolated Data -y Partial Fourier reduces scan time at the cost of increased noise (reduced SNR) Spatial Resolution is Unaffected “Physics of Clinical MR Taught Through Images” V. Runge, Thieme Medical Publishers, 2005 Slide # 87 Slide # 88 Zero Fill Zero Fill Scan Time = TR x Ny x NSA Scan Time = TR x Ny x NSA Ky 256x 128y 256x 256y Ky 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 000 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 000 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 000 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 000 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 000 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 000 Reducing Ny Reduces Scan Time Reduces Spatial Resolution Increased SNR Increases Truncation Artifact * Note: the number of phase encodings may be selected by scan percentage Image courtesy Dr. Val Runge Slide # 89 Slide # 90 15 Rectangular FOV Rectangular FOV Scan Time = TR x Ny x NSA Scan Time = TR x Ny x NSA Standard Acquisition + 128 ky 50% Rectangular FOV ky + 128 ky ky Phase 0 ky 0 ky - 128 ky - 128 ky 240 FOV / 256p 120 FOV / 128p rFOV reduces scan time at the cost of increased noise (reduced SNR) Reduces Ny - reducing scan time Increasing "step" between phase views reduces pFOV Slide # 91 Slide # 92 Parallel Imaging Conventional Spin Echo •Scan time is reduced by using a Image courtesy Dr. Val Runge rectangular FOV (therefore spatial resolution is maintained) •Data from multi-channel / phased-array coils is used the image reconstruction process •Some techniques require a "reference" or "calibration" scan prior to the actual scan •Image is reconstructed with the prescribed FOV + 128 ky Gy 0 ky kx Gx - 128 ky -128, -127, -126....-1, 0, +1, +2 ... +126, +127, +128 Slide # 93 Slide # 94 Fast Spin Echo Scan Time Conventional Spin Echo 4 ETL Example Fast Spin Echo TR x Ny x NSA + 128 ky 0 ky ETL 128 phase 160 phase 192 phase 256 phase Gy •Conventional Spin Echo fills one "line" of k-space per repetition of the pulse sequence •Fast Spin Echo fills multiple lines of k-space per repetition of the pulse sequence •The number of lines filled per repetition period is determined by the Echo Train Length (ETL) •The TE most effecting image contrast is placed in the more central "lines" (effective TE) TR x Ny x NSA kx 10 ETL 14 ETL 17 ETL 25 ETL Scan time increases with increasing spatial resolution (phase) Scan time shortens with increasing ETL Scan time shortens with reduction in spatial resolution (phase) Image "blurring" can increase with increasing ETL - 128 ky Image Courtesy Siemens Medical Systems Slide # 95 Slide # 96 16 Echo Planar Imaging (EPI) Benefits of Fast Spin Echo Sample Scan Time TR x Ny x NSA 3000 TR x 256 phase x 2 NSA = 25.6 minutes ! Same scan with FSE and ETL of 16 = 1.6 minutes !! 500 TR 1500 TR 3000 TR 5000 TR Images with bright fluid often show pathology best due to presence of water The long T1-relaxation time of water requires longer TR times to obtain images with bright fluid Scan time increases with increasing TR Slide # 97 Slide # 98 EPI Speed Compared to FSE Summary Scan Time = TR x Ny x NSA FSE FSE 180 180 echo echo 180 180 echo echo 180 180 echo echo 180 180 echo echo 90 90 How many lines of acquisition? Zero-fill EPI EPI 180 180 echo echo echo echo echo echo echo echo echo echo echo echo echo echo Reduced NSA Partial Fourier 90 90 Rectangular FOV (Parallel Imaging) SS-EPI 4 sec whole brain (1.5T) FSE 25 sec whole brain (3T) Reducing scan time by altering the way k-space is filled typically reduces either spatial resolution or SNR QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Slide # 99 Since reduced spatial resolution is almost always undesirable, therefore, most advanced imaging techniques are SNR starved 6 Slide # 100 6 Outline • Imaging Matrix • Gradients & Signals • Phase, Frequency and Amplitude • Slice selection • Phase encoding • Frequency encoding 6.1 MR Image Formation Matrix, Gradients & Signals Image formation & k-space Thank you for your attention! Click to take your post test and get your credits Carolyn Kaut Roth, RT (R)(MR)(CT)(M)(CV) FSMRT CEO Imaging Education Associates candi@imaginged.com www.imaginged.com Slide # 101 17