User Manual for CREANUIS
Contents
1. generalization of an angular spectrum method GASM allows to consider media with an inhomogeneous coefficient of nonlinearity and the simulated field will impact the final RF image simulation Efforts on the computation time have been made on the nonlinear field with a version of the software working on GPU graphic processing unit 3 1 2 Software description CREANUIS has been designed in C C in order to perform a quick simulation of the nonlinear propagation and of the RF images An interface is proposed in Qt but can also be disabled In the GASM simulations the Fourier transform are performed using the FFTW library 4 or the cuFFT library when the GPU programming is used Some accompanying files are proposed to load the simulated data with Matlab The structures of the saved data are detailed hereafter and the image can also be loaded with another program as soon as an interpreter is designed 2 Installation 2 1 Windows On windows the provide package install the various required exe and dll files The vcredist_x86 if not present on the system has also to be installed During the installation of CREANUIS the path of the installation has to be change do not used Program Files directory because last windows operating system forbids to write in this directory Additional Matlab files are given in the installation direction Three folder are also generater where the CREANUIS programm is install and are required to correc2. some messages are displayed in the terminal If 1 is selected the debug messages corresponding to the RF image reconstruction are displayed With 2 the messages of the GASM simulation are also displayed In the G1 menu settings can be saved or loaded in the action menu The help menu displays a link to the CREANUIS web site and the licence specification The save load actions save or load the data in the save settings txt file This file is created readed in the path directory G2 TREN Jo G1 Path buse D Matlab CREANUIS Soft pressure_field a_default Name of the nirf File image_no_name G5 LAUNCH CREANUIS G6 G2 G3 G4 Message level Fig 1 Illustration of the general settings of the CREANUIS interface Interface description Probe space and beamforming strategy 3 2 Probe space and beamforming strategy The first part of the interface Fig 2 allows to specify the probe geometry P the medium characteristics M and the beamforming configuration B All these parameters are saved in the save setting txt file In the B menu the user can save the pre beamformed data In that case for each RF line all the elementary received RF lines on each active element are saved The user has to take care of the large size of the resulting nonlinear RF data that can be generated Currently only linear arrays are simulated with CREANUIS In a future version of CREANUIS more complex arrays are going to be taken into
3. User Manual for CREANUIS User Manual of CREANUIS Introduction General overview Table of Content CO OR ee ee een ee een ee 5 LIL GENE lo Ve ea na Renee 5 1 2 SOrtware Des CHOCO en een 5 2 IMST LEI a E O E A E E E E E A A E EE 5 AN OO ea ee bo a OEEO or 5 2 2 Linux Fedora distribulion en nennen inner 5 As CP OO a ee a ee ee 6 3 Mercedesi EOI ee EEEE EEEO Ean 6 3 1 GENE SENE S ee nee cn 6 3 2 Probe space and beamforming strategy 7 3 3 Scatterers and GASM configuration sise 7 52 Depay resus ne ne a on cie dan a 9 4 DOS SCOR ee aan tie dt a eu dis 9 M N S ee 9 A42 Nonlinear COG ICONE ARS a a de an be a ne 10 SOS RES OS net ee ea en ee IVE 10 5 Utilization of CREANUIS in command line iii 10 6 Accompanying Matlab files ins 11 7 ICE a a a E A E EE ee 11 8 PIOIOI IN ee ee AA 11 User Manual of CREANUIS Introduction General overview Introduction 1 1 General overview CREANUIS is a tool that simulates nonlinear radio frequency RF ultrasound images It is the combination of two specific tools The former is a nonlinear ultrasound propagation simulator that allows to compute the evolution of the fundamental and second harmonic wave 1 Then using this field information a reconstruction algorithm creates the corresponding nonlinear radio frequency RF image 2 The resulting RF image contains the fundamental evolution but also the second harmonic one The design of the nonlinear propagation simulator which is a
4. account For the attenuation a frequency dependent law has been chosen because the second harmonic wave is faster attenuated than the fundamental one 5 Initial parameters Medium Definition Display results Probe Settings P Transmission Reception setting B 245 Pitch um 3 Central Frequency MHz 30 Kerf um 100 Sampling Frequency MHz 6 Height mm 3 Number of Cycles 64 Number of Active Elements 0 Phase Number of Lines 163 100 Initial Pressure kPa None v Window Medium Settings M 23 Elevation Focus mm 1000 Density kg m3 Transmit Focus x y 2 mm 1540 Speed of sound m s 0 0 0 Attenuation frequency dependent None Apodization in Transmission 0 002 Attenuation Np m Mhz None M Apodization in Reception 2 Gamma _ Save Prebeamformed Data Yes No Fig 2 Illustration of the probe medium and beamforming settings in the CREANUIS interface 3 3 Scatterers and GASM configuration In this second thumbs Fig 3 the scatterers of the medium S and the nonlinear map NL are configured In the scatterers part S the dimensions of the space where the scatterers are placed are defined with the maximum lateral and elevation distances In the z direction the minimal and maximal depths to reach are defined These depths are the one used in the final image creation The scatterers density N allows to quickly select the number of scatterers per resolution cell However in some cases this nu
5. ded in CREANUIS 3 4 Display results menu This last thumb Fig 4 is the display interface It allows to see the nonlinear coefficient the pressure field or the nonlinear RF nIrf file The different buttons allow to select some other file and to quickly visualize the different results D1 allows to display the current nonlinear coefficient map D2 to load an existing pressure field and D3 to load an exiting nirf image For the last two the fundamental and second harmonic component is displayed in the left and right part of the thumb Initial parameters parameters Medium Definition Medium Definition Display results results Display Beta Parameter Display Pressure Field Display nirf Image D1 D2 D3 Fig 4 Illustration of the display thumbs and the possibility to visualize the nonlinear coefficient the pressure field and the nonlinear image 4 Data structure 4 1 Nlirf files The nirf file is the output format of the nonlinear RF image that is computed by CREANUIS The file is a binary file only writen with floats numbers A header of 18 floats is present The header different data are saved in the following order User Manual of CREANUIS HEADER Transmitted frequency sampling frequency speed of sound initial pressure density pitch kerf height number of elements number of points on one RF line third dimension of the RF image different of 1 if the pre beamformed data are saved number of active elements transmi
6. ers need to configure CREANUIS If the setting file is not placed in path_name directory an error is return by CREANUIS scatterers scatterers_file the user must specify the file where the scatterers position and amplitude are saved Using CREANUIS in command line did not yet allow to used the classical random diagonal grid distribution This file can be generated using the accompanying Matlab file Optional arguments nonlinearity nonlinear coefficient file if a specific nonlinear coefficient medium is desired it has to be generated previously If the nonlinearity tag is not present a nonlinear coefficient medium of B 3 5 is used in the GASM simulations debug debug number if the output messages are desired in the terminal a number above O has to be selected The number are the same as the graphic use of CREANUIS Let recall 10 Accompanying Matlab files Scatterers files that the tag do gasm in the save setting txt has to be equal to 1 to do the GASM simulations 6 Accompanying Matlab files With CREANUIS several accompanying files are proposed to be able to use the produced results in a Matlab interface The files are divided in two categories and are summarized in Table 1 Files to read information saved by CREANUIS Files to write information that can be read by CREANUIS Table 1 List of the accompanying Matlab files read _ nonlinear _coefficient_file m write nonlinear _ coefficient _file m read
7. l 11 User Manual of CREANUIS 2 F Varray C Cachard P Tortoli and O Basset Nonlinear radio frequency image simulation for harmonic imaging CREANUIS in EEE Ultrasonics Symposium San Diego 2010 3 F Varray C Cachard P Tortoli and O Basset Simulation of 3D t nonlinear pressure field propagation on GPU with the Angular Spectrum Method in IEEE Ultrasonics Symposium Orlando 2011 4 M Frigo and S G Johnson The Design and Implementation of FFTW3 Proceedings of the IEEE vol 93 n 2 pp 216 231 2005 5 T L Szabo Generalized Fourier transform diffraction theory for parabolically anisotropic media The Journal of the Acoustical Society of America vol 63 n 1 pp 28 34 1978 12
8. mber is directly the number of scatterers in the medium For example with the diagonal vertical or PSF configuration exactly N scatterers are used in the medium Moreover with User Manual of CREANUIS the grid scatterers configuration a grid of N x N is design to simulate the medium The backscattering amplitude follows a normal distribution The scatterers distribution can also be imported from a file Concerning the GASM configuration NL the discretisation in the x y and t axis is performed in the definition of the 3D matrix in the GASM simulation The discretization of the z axis defines the different incremental step in the computation of the second harmonic field Then the obtained field is interpolated using the interpolation dimension on the z axis In the right part some pre configured situations of nonlinear coefficient map are proposed The default map is a constant medium with B 3 5 Then by clicking on the add button the user modifies the map using a new B value The different checkable boxes have different actions Compute one way field if selected only the GASM simulation is performed no impact of scatterers and image creation The field is saved with the same output name as the nirf image but in the current path Compute GASM if selected the GASM simulations are conducted Otherwise the saved field in the current folder is loaded This option is useful to save computation time when the field has already been sim
9. scatterers file m write scatterers file m read image _rf m write image rf m read field m write apodization m The action of each file is detailed in the help header of the Matlab file If specific apodization scatterers or nonlinear medium are required it is recommended to use these files 7 Licence The CREANUIS software has been placed under the CeCILL B licence This licence gives to the user the authorization to use CREANUIS and to publish works obtained using this software The only condition is to cite in each work where CREANUIS has been used the following publications F Varray A Ramalli C Cachard P Tortoli and O Basset Fundamental and second harmonic ultrasound field computation of inhomogeneous nonlinear medium with a generalized angular spectrum method EEE Transactions on Ultrasonics Ferroelectrics and Frequency Control vol 58 no 7 pp 1366 1376 2011 F Varray C Cachard P Tortoli and O Basset Nonlinear Radio Frequency Image Simulation for Harmonic Imaging CREANUIS IEEE International Ultrasonics Symposium San Diego USA pp 2179 2182 2010 8 Bibliography 1 F Varray A Ramalli C Cachard P Tortoli and O Basset Fundamental and second harmonic ultrasound field computation of inhomogeneous nonlinear medium with a generalized angular spectrum method IEEE Trans Ultrason Ferroelectr Freq Control vol In press 2011 4 http www cecill info licences Licence_CeCILL B_V1 en htm
10. tly executing the software input nirf file pressure_field 2 2 Linux Fedora distribution On Fedora distribution the tar gz file has just to be extracted Then the program can directly be used The same directories as in the Windows installation are created and required http gt nokia com products http www fftw org http developer nvidia com cuda downloads User Manual of CREANUIS 2 3 Created folder Three directories are created by the install files and are required in the same root direction The input folder is used to save some user inputs All the created nonlinear radio frequency nirf images are saved in the nirf file folder The field the nonlinear coefficient map and the settings if saved are saved in the pressure_field folder 3 Interface description The CREANUIS interface is divided in three distinct thumbs coupled to some general settings 3 1 General settings In the general settings Fig 1 the user can defined the path of the working directory of CREANUIS G2 By default this path is set to the directory where the CREANUIS exe file is located with the addition of the directory pressure field a default This path can be changed using the button G3 In the box G4 the name of the output file can be chosen If the file exists in the nirf file directory it replaces the previous nirf file The G5 button launches the simulation The box G6 corresponds to the debug level wanted If O is chosen just
11. tted focus z direction elevation focus minimal depth maximal depth number of transmitted cycles transmitted phase in degree Then the other elements correspond to the amplitude of the RF image The dimension of the radio frequency image is given by the number of probe element by the number of points on one RF line by the number of active element if pre beamformed image is saved 4 2 Nonlinear coefficient files The nonlinear coefficient file is a binary file that contains first two entire N and M and then NxM float elements To create a nonlinear coefficient file such configuration has to be used in order to be understood by CREANUIS 4 3 Scatterers files The scatterers file is a binary file that contains first an entire N and then the position and the amplitude of each scatterer in float The rest of the file is successively composed of the N positions x the N positions y the N positions z and the N amplitude values To create a scatterer file such configuration has to be used in order to be understood by CREANUIS 5 Utilization of CREANUIS in command line CREANUIS can be used in command line in order to suppress the graphic interface and then launch the simulation in a cluster for example To do this some arguments have to be added after the CREANUIS is launched Obligatory arguments path path_name the user must specify the path where the save_settings txt file is backup in order to access to the entire paramet
12. ulated Save all the fields if selected the fields computed are saved Use GPU if selected the GASM simulations are conducted on the GPU if it is correctly initialized Initial parameters Medium Definition Display results Scatterering Medium S 25 Maximum Lateral Distance mm 10 Density of reflectors z Maximum Elevation Distance mm Random v 20 Minimum z Axis mm Save Reflectors Data Yes No 80 Maximum z Axis mm Nonlinear medium definition dimension nonlinearity NL 128 Discretisation on x Axis Add Inclusion in the Nonlinear Medium Bubbles x 6 64 Discretisation on y Axis 256 Discretisation on t Axis _ Compute One Way Field Yes No _ Compute GASM Yes No start at line 0 2 5 dz discretisation in GASM mm Save all the Field Yes No 200 Interpolation dimension on z Axis Use GPU if possible Fig 3 Illustration of the scatterers definition and the GASM configuration Existing nonlinear coefficient map can be imported by the user The dimension of the imported image has no impact because interpolation is used in the field simulations However it has to be considered that the dimension of the map is set by the probe and space parameter Indeed the Data structure Display results menu nonlinear map will have a dimension in the lateral dimension Niine Pitch Nine Pitch and in the axial dimension 0 z max The number of points that composes this image has no impact once loa
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