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Segment - Technical Manual

1. gt Unit calls unit Called from GUI Figure 5 Overview of the internal structure of the Report function superunit and transaction analysis 125 CHAPTER 15 UNIT IMPLEMENTATION Datastructure The information used to build a 3D model is contained in SET struct Number of stack to report is taken from NO variable Functions init report3dmodelrotated Display 3D model of rotated image stacks rotatedplothelper xc yc linecolor Helper function to display segmentation in rotated image stacks 15 5 2 Report Volume unit The purpose of the Report Volume unit is to do volume reports Interactions The Export unit is called for export of data Datastructure The volume information is taken from the SET struct Number of stack to report is sometimes taken from the NO variable Functions curve_Callback no GUI for reporting the volume curve loop_Callback Reporter for volume loop not yet implemented 15 5 3 Report Radial Velocity unit The purpose of the Report Radial Velocity unit is to do reports of radial velocity 126 15 5 REPORT SUPERUNIT Interactions Suitable image stacks are found by the Find unit and the calculations that generate the reported results are performed by the Calculation unit The Export unit is called for export of data Datastructure The radial velocity information is taken from the SET struct Number of stack to report is taken from the NO variable Func
2. certmap smootht2map calccertmap t2map resmap mask smoothf smooththres Calculate certainty map t2map kmap resmap globalt2 S k calcmap no mask thres Calculate T2 T2 map and other maps 207 CHAPTER 15 UNIT IMPLEMENTATION calemask Calculate mask depending on selection of regional restriction myocardium ROI s or full image climedit_Callback Callback for edit box of display limit climslider_Callback Callback for slider to set display limit close_Callback Close GUI colorbarhelper Helper function to display colorbar createimagestacks_Callback Output of image stacks containing raw T2 T2 map smoothed T2 T2 map and resolution map endline Buttondown Buttondown function for line indicating end of time period to fit endline_Buttonup Buttonup function for line indicating end of time period to fit endline Motion Motion function for line indicating end of time period to fit export _Callback Export data to clipboard globalfit_ Callback Plots a global fit plot ignore ignorehelper s no thres Check which points to ignore init visible Initialize GUI 208 15 10 ANALYSIS SUPERUNIT magpoint_Buttondown User clicked on image gives show fit magpoint_Buttonup Buttonup function for magpoint in image magpoint_Motion Motion function for dragging magpoint in image recalc_Callback Recalculate all maps and make graphical updates restriction_Callback type Callback for
3. Tools to send DICOM files to the hospital PACS system 27 CHAPTER 10 ARCHITECTURAL DESIGN Tools to search in the hospital PACS system Tools to convert between different DICOM formats e Justification for using the SOUP element A program was needed for sending and recieving DICOM files to the hospital PACS connec tion OFFIS DCMTK toolkit is vendor independent and is already established and used by hospitals e Documentation to end user Technical documentation this sec tion e Method to ensure appropriate use The DCMTK library are in cluded in the general software package and do not need any processing by the end user e Method to ensure the SOUP element works The verification of the DCMTK are included in the software testing e Control the SOUP element The software comes in complete source code and is available as open source software There is an open dis cussion forum about the software but no support agreement for the software The DCMTK library is only upgraded to access bug fixes or when new features useful in Segment are released Known SOUP issues In this section only issues that potentially affect us are listed e The key option in findscu and movescu does not work See FAQ 43 in order to fix this bug Workaround is employed Not affecting us after this e There is a memory leak in the extended negotiation code only occur ring if that feature is actually used This feature is not used
4. Testing broken callbacks 18 Compiling Segment radicada bck BS e 18 2 Running the compilation script 18 3 Configuring o eee dara a a a 184 Multi platform support exito dores eh Heda de Ae ee EEE fees gees ee eek ee ee 19 How to Create Own Plug ins 20 Segment User Community Bibliography viii 237 237 237 238 239 240 240 243 245 247 1 Regulatory status Segment may be used for either investigational off label use or commercial purposes Please see license terms which license form that apply to you Users are also required to investigate the regulatory requirements pertinent to their country or location prior to using Segment It is in the users respon sibility to obey these statues rules and regulations 1 1 Commercial usage of Segment FDA approved versions of Segment are identified with a labelling upon start up displaying licence details and the FDA 510 k number K090833 If your version does not display this information your version is not FDA approved and you need to contact Medviso AB to receive a such license Please note that there are features that are not included in the FDA ap proval These functions are marked in this User Manual that they are only for investigational use 1 2 Indications for use Segment is a software that analyzes DICOM compliant cardiovascular im ages acquired from magnetic resonance MR scanners Segment specifically analyzes the func
5. Timer used in cinewindow Used in the automatic LV segmentation for MR images Used in the automatic LV segmentation for MR images DynamicPACS Stores PACS details specified through API by an external program 43 13 SET Variable This global variable is probably the most important variable structure since it contains all image data and all measurements The variable is a struct array As an example SET 2 refers to the second image stack SET 2 CurrentTimeFrame refers to the field that contains the current time frame of the second image stack The function loadfieldhelper is used to control backwards compability in the SET struct When adding new fields it is essential to also update this function Below a list of all fields are given AccessionNumber DICOM tag Accession Number AcquistionTime DICOM tag AcquisitionTime AutoLongaxis True if the amount of long axis compensation should be automatically calculated See Reference Manual for details BeatTime Controls how fast one heart beat is played when playing images as a movie Originally set to 60 HeartRate May be adjusted with the slower faster icons CenterX Position of the center mark CenterY Position of the center mark Children List of numbers of image stacks that are children of derived from this stack Colormap This field contains a colormap 256 x 3 vector When the image is grayscale it is an empty field 45 CHAPTER 13 SET V
6. drawfunctional draw the funcitonal image stack drawfusion draw the fusion image stack res findtwo2 curve point find the two closest points in the input variable curve to the point in the input variable point flip_Callback flipparameter flip the functional image and update the new images functionalcolor_Callback change colormap in the functional image stack init_Callback starts the fusion gui keypressed fignum evnt move in the image slices with the keyboard arrows move_Callback button read in translation and rotation plotval plotvalues position myocardium zvalues t find and return the endo and epivalues to plot resamplefunction param1 param2 param3 resample the functional image to the same size as the anatomical image also rotate and translate the functional image reset_Callback reset to the start position of the functional image resetcontrast_Callback reset the contrast and brightness to the start values savedefault_Callback save the current translation rotation flip and colormap in a default mat file 228 15 10 ANALYSIS SUPERUNIT plotval segmentation set1 set2 nr parameter t return the endocardial segmentation in the anatomical and functional image stacks setdefault_Callback apply the default mat file including settings for translation rotation flip and colormap to the current functional image stack settransparent transparent parameter set the intensity b
7. getpathinfo Scans directory and builds a structure of relevant information The function populates the file listbox and stores DATA Preview FileList variable If there is a directory return the number of files If it is a file simply the filename Later add also if it is selected The generated information is stored in the file folders cache in every folder Segment visits This function also handles saving loading and regenerating this cache when needed hasdcm description getseriesdescription folder varargin Assumes that folder is a folder with a DICOM image series one or more dicom files In the second optional argument a list of files in the directory can be passed in the same format as the matlab builtin dir returns This is useful when a dir this function needs the results of one is expensive such as when listing very large directories on a network share why this is expensive nobody knows Searches for the first dicom file and creates a nice string with a description max maxlength characters long Used in getpathinfo hasdcm is true if a dicom file was found false otherwise If hasdcm is false Unknown is returned If the function can t come up with a nice description Unknown is returned 181 CHAPTER 15 UNIT IMPLEMENTATION initset no Initialize the set structure keypressed fignum evnt Helper function to handle keypressed events loadandmerge_Callback Loads one image at
8. If not Remap according to indexed grayscape Unless An external colormap has been supplied then use that This is used to force truecolor grayscale by passing true to RETURNMAPPING c b are contrast brightness settings used by contrast Callback when doing realtime update during mouse motion See RETURNMAPPING above xnew ynew resampleclosedcurve x y n method distributed General helper fcn to resample a closed curve xnew ynew resamplemodel x y n method distributed y p gt bi 9 Resample the a stack of contours typically segmentation to different number of points n map returnmapping no forcetruecolor If SET no Colormap exists Returns truecolor colormap for this If not Returns grayscale 1 D indexcolor map Unless forcetruecolor is true then 3 D truecolor grayscale is returned regardless of SET no Colormap See REMAPUINTS below 109 CHAPTER 15 UNIT IMPLEMENTATION pos rlapfh2xyz no rl ap fh Convert from RL AP FH coordinates to Segment internal coordinate system x y sax2gla xi yi zi no Convert image coordinates from short axis to GLA view im truedata2im z no Inverse of calctruedata volume_helper no Helper to find peak ejection and empty volumes etc Lots of checks to prevent NaN or Inf to be presented when some of the data are missing contrast brightness win2con window level no 9 g 9 9 Inverse of con2win pos xyz2rlapfh no x y z Converts from segment
9. This constant will be implemented in later versions of the module 14 12 1 Calculating fitting error The fitting error is calculated as the error of the reconstructed signal minus the true signal value for each pixel and echo time The error for each pixel is calculated as the mean of the absolute value of the percentage errors for all echo times 14 12 2 Smoothing The smoothing process is done by normalized averaging where the certainty of each pixel is taken into acount to avoid the effect of uncertain pixels 6 The smoothing kernel is a Gaussian smoothing kernel illustrated in Figure 4 The certainty is calculated linearly as a function of the error measure calcu lated in Section 14 12 1 Pixels with an error with 25 or more are assigned a certainty of zero and pixels with zero error are assigned a certainty of one The cut of value of 25 is taken from 7 Pixels where the T2 T2 value is negative is also assigned a zero certainty The normalized averaging is cal culated by first calculating a filtered version of the T2 T2 map multiplied with the certainty as M T C F 13 73 CHAPTER 14 IMPLEMENTATION DETAILS Figure 4 The filter used for smoothing where T is the raw T2 T2 map is pixelwise multiplication denotes convolution F is the smoothing filter kernel illustrated in Figure 4 and M is a temporary map used to calculate the final smoothed T2 T2 value as T M C F 14 where T is t
10. b blue line y yellow dotted line e Area area of the ROI for each timeframe e Mean mean intensity of the ROI content for each timeframe e StD standard deviation of the ROI content for each timeframe Related are also the fields RoiArea RoiCurrent and RoiN 163 CHAPTER 15 UNIT IMPLEMENTATION Functions removefromallbutthistimeframe n Remove ROI from all but this time frame removefromthistimeframe n Remove ROI from this timeframe roi_Buttondown panel button down function for drawing roi roiaddfixsize_Callback Function for adding roi with fix size roiaddinsector_Callback angle width percentfromendo percentfromepi numsectors name Add sectors in ROI input arguments is angle of where to start the width of the sector given as an angle how many percent from endo the sectors will be placed how many percent from epi the sectors will be placed the number of sectors and finally the name under which the sector roi will be stored name roiasklabel varargin Lets user pick name of roi from a picklist Input roitoname is the number of the roi to name if this input argument is empty the choice of naming the roi to ROI n is disabled the function can not handle a cell so if multiple rois are to be named use as first input roinamein is the name of the roi to be renamed this functionality is used when renaming using template Both input arguments are optional but if the fir
11. measure_Buttondown panel Button down function for placing measurements measure_Motion ind Motion function for measurements measureexport_Callback Export measurements measuremove_Callback dx dy Helper function to move measurements measurepoint_Buttondown panel Buttondown function when clicking on a measurement point marker measureput_Buttonup Called when a measurement point except the endpoint is placed measureshapeexport_Callback Export measurement shape mmodel_Buttondown panel Called when mmodel is pressed down sets motion and buttonup function mmodel_Motion Motion function of the first mmode point mmodelline_Buttondown panel Called when mmodelline is pressed down sets motion and buttonup function 81 CHAPTER 15 UNIT IMPLEMENTATION mmodelline_Motion Motion function of the first mmode line mmode2_Buttondown panel Called when mmodel is pressed down sets motion and buttonup function mmode2_Motion Motion function of the second mmode point mmode2line_Buttondown panel Called when mmodelline is pressed down sets motion and buttonup function mmode2line_Motion Motion function of the second mmode line mmode_Buttonup This function is called when buttonup occurs after draging one of the mmode objects mmodecenter_Buttondown panel Called when mmode center is pressed down sets motion and buttonup function mmodecenter_Motion Motion function of the mmode center point
12. ARCHITECTURAL DESIGN 10 1 List of superunits This list provides references to sections of chapter 15 where the superunits are documented and further divided into primitive units It also references ID s of requirements that are fulfilled by the unit Main superunit RA14 RA15 File superunit 15 9 RB1 RB2 RB3 RC1 RC2 RC3 RE1 RE2 RG1 RG2 RG3 RI Draw superunit RA4 RA5 Calc superunit Resources superunit Segmentation superunit 15 6 RA6 RA7 RA19 RA20 Tools superunit Analysis superunit RA12 RA21 Report superunit 15 5 RA16 RA17 RB4 Helper functions superunit 10 2 OTS software and SOUP elements 10 2 1 OTS software The Off the shelf software OTS software used by Segment is Matlab Com piler Runtime MCR which has the following specifications 26 Manufacturer Mathworks Version R2014a Hardware specifications MCR takes about 450 MB harddisk space Software specifications Opearting system Windows 2000 or later both 32 bit and 64 bit are supported Intended use MCR is the runtime environment for the Matlab devel opment language Segment is precompiled by using Matlab Compiler The compiler converts the code to encrypted pre parsed code that is interpreted by MCR which is installed together with each copy of Seg ment 10 2 OTS SOFTWARE AND SOUP ELEMENTS Features Execute Matlab files without an installed version of Matlab on the computer Justification for using the OTS soft
13. Interactions This unit calls the Flow quantification unit to access the flow data used to determine separation in time of the pulse wave Datastructure The measurement information is taken from the Measure field and the ROI information for flow analysis from the Roi field of the SET struct Functions close_Callback Close Pulse Wave Velocity GUI export Export data to clipboard getflows Get values of flow calculation from Flow report init Initiate Pulse Wave Velocity GUI sigmaslider_Callback Callback for when using slider to change the value of sigma updateaorticimage Update full view image of aorta updateflowplots Update plot of flow curves 135 CHAPTER 15 UNIT IMPLEMENTATION 15 5 8 Qp Qs Valve unit The purpose of the Qp Qs Valve unit is to provide the user with tools for reporting Qp Qs and valvular analysis Interactions This unit calls the Flow quantification unit to access the flow data used to determine Qp Qs or regurgitant fractions Datastructure The ROI information for flow analysis is taken from the Roi field of the SET struct No datastructure is updated by this unit Functions svaorta svpulmo fwaorta bwaorta fwpulmo bwpulmo getsv Calculate and return stroke forward and backward volumes both for the aorta and the pulmonary artery result qpqs Calculate Qp Qs and display result in a message box mitrfrac tricfrac mitrvol tricvol regurg Calculate regurgitant fract
14. QrQ 8 14 10 Infarct size extent and transmurality Calculations of infarct sizes etc are based on counting pixels i e each pixel has a binary classification There are two methods for regional analysis available one are based where the percentage of the pixels that are inside the sector The other method is based on radial spikes from the center endo or epicardial depending on setting in the preferences The line between en docardium and epicardium is resampled in 50 steps and the percentage of infarcted pixels are counted 71 CHAPTER 14 IMPLEMENTATION DETAILS Infarct extent is defined as the projected infarcted area on the endocardial surface 4 Lua a 9 i where Tert is the infarct extent T is the transmurality of sector i and R is the mean endocardial radius of sector i 14 11 Number of SD from remote for Scar The number of SD from remote for an existing scar segmentation is calculated by the function found in the main menu in Segment under MR menu Viability menu and then the menu option Get SD from Remote The presented value is calculated by first calculate the mean and sd in the remote area Meanremote and SDremote If there exist ROIs named Remote ROI these regions define the remote area Otherwise the whole myocardium except for the scar re gion defines the remote area The presented SD from remote value is then calculated by Loptim Mednremote S Dpremote SD fromRemote 10 T
15. Takes care of segmentation 177 CHAPTER 15 UNIT IMPLEMENTATION newvol upsampletemporal f vol varargin Helper function to upsample in time f is factor and vol is volume to upsample Third argument is optional and is type 1 image 2 segmentation default upsampletemporal_Callback f Usamples current image stack in time f is upsampling factor Takes care of segmentation newvol upsamplevolume f vol silent Helper function to upsample a volume vol viewpatientinfo_Callback arg no GUI to view and adjust patient information viewtrueintensity_Callback View true image intensities in current timeframe and slice 15 9 File superunit The File superunit contains functions for loading saving transferring and doing operations on files An overview of its subunits and how they commu nicate is provided in Figure 6 15 9 1 Open File unit This is the GUI part of the file loader Interactions This function interacts with e Main Segment superunit segment main with the renderstacksfromdicon setting title clearing SET variable and other preparations for loading data enabling and disabling GUI options e Tools superunit with normalization e Image file reader unit to do the low level data reading 178 15 9 FILE SUPERUNIT Segment Server Filemenu External PACS Openfile Image file reader gt Unit calls unit Called from GUI Figure 6 Overview of the inter
16. drawing of colour overlays indicating regions of manual corrections Calls to reshape2layout e Helper functions superunit Find slices with endocardial and epicardial segmentation in which the scar segmentation can be performed Handle mouse interaction when drawing scar manually e Calculation superunit Volume calculations of scar finding slices cre ating masks Volume unit Datastructure The data is stored in the Scar field of the SET struct e IMcontains the image itself a copy This is from historical issues and may be removed in future versions e Auto a logical array that contains true in the positions that the algo rithm marks as infarcted e Manual an int8 array that contains 1 for the pixels that the user have manually to be infarcted and 1 for the pixels that the user have marked as non infarcted 157 CHAPTER 15 UNIT IMPLEMENTATION e Result a logical array containing the final viability delineation with the manual corrections e NoReflow a logical array containing one in the regions that have been identified as no reflow regions or regions with microvascular obstruc tion e MyocardMask a logical array containing true in the myocardium and false otherwise e beta a scalar controlling the ruffness of the surface See the algorithm description for further details 11 e stdlimit a scalar determine the number of standard deviations from remote to take e radius Radius of the fast level set
17. flowplotquiver_Callback Plots a quiver plot of current image stack flowpropagate_Callback m Propagate a flow ROI to next time frame and refine flowrefine_Callback m silent Refine segmentation of a flow ROI 128 15 5 REPORT SUPERUNIT flowsegmentroi_Callback name Do segmentation of a flow roi flowsetvenc_Callback Set VENC for current image stack flowshrink_Callback m factor Shrink a flow ROI flowtrackroi_Callback m Track a flow ROI through all time frames varargout flowvesselenhancement no Beta function to show vessels with time depending flow setflowpreferences_Callback open a box where it is possibly to set the ROI propagation parameters balloon force edge force and curve force close_Callback Close flow report GUI export Export flow data to clipboard flowbar_Buttondown type Button down function for flow bar in flow report GUI flowbar_Buttonup type Button up function for flow bar in flow report GUI flowbar_Motion Motion function for flowbar varargout getdata arg Output requested data from flow calculations ok init no Init flow report GUI recalculate no Calculate flow data update Make graphical update of plot zoom Callback for checkbox toggling zoom on off 129 CHAPTER 15 UNIT IMPLEMENTATION 15 5 5 Report Slice unit The purpose of the Report Slice unit is to do slice based reports of regional function Interactions The Export unit is c
18. 0 updatesliders Updates the time and slice sliders to reflect current positions updatetemporalplotaxes Updates the temporal plot of the current pixel updatetextelements Updates all text elements in the GUI updatevelocityimage Updates the axes showing the velocity image updatevelocityimagezoomandpan Updates zoom and pan in the velocity image 140 15 5 REPORT SUPERUNIT velocityimage_ButtonDown Callback for clicks in velocityimage zoompushbutton_Callback inout Zoom pushbuttons Change zoom level update GUI 15 5 10 Report Sheet unit This unit is used to generate a comprehensive patient report It consists of the m file reportsheet m the superclass definition htmlgenerator m used for formatting the output into a HTML page and its subclass definition figgenerator m used for formatting the output into Matlab figures that can then be converted into image files for exporting data to PAF or PACS Interactions This unit calls other units from the Report superunit to insert their data into the report sheet One such unit is the Flow unit Another is the Report Bullseye unit The File superunit is called to generate reports in DICOM format and upload them to PACS Datastructure This unit uses the field Report of the SET structure to contain information of what to include in the report and the field PatientInfo to contain patient information used in the report Functions adddistances report Adds distance
19. 10 3 Protected code sections Some of the building blocks contains propriety algorithms and will only be made available as p code i e platform independent precompiled Mat lab code The blocks that are be hidden are lv m rv m viability m flow m pacs m patientdatabase These functions will not be described in great detail in this document for documentation of these files please see 28 10 4 GLOBAL VARIABLES AS DATA COMMUNICATION internal documents at Medviso AB 10 4 Global variables as data communication Segment uses two global variables to store the state of image data graphical handles These two variable are SET and NO The structure of the variable SET is documented in Chapter 13 The variable DATA can be seen as a global variable but is a global object This allows for overloading the entire user interface of Segment The DATA object contains global state of the program and all main graphical handles and is documented in Chapter 12 The global variable SET contains all image data segmentation ROI s mea surements annotation points etc The variable NO is simply a scalar and points to the current image stack It is highly recommended not to use the global NO but rather include this in the call The reason for having global variables instead of a completely functional programming approach is that e Simplicity for writing plug ins e Execution speed Using this approach there are way less variables point
20. 15 4 HELPER FUNCTIONS SUPERUNIT y existendoonlyinedes no True if endocardium exists in ED and ES slices y existepi no True if epicardium exist in some slices y existepiinselected no t True if epicardium exist in selected slices If argument is specified only look in timeframe t y existepiinslices no t True for the slices where endocardium exists If argument is specified only look in timeframe t oterwise look if there is endocardium in any time frame y existepionlyinedes no True if epicardium exists in ED and ES slices y existrvendoinselected no True if RV exist in selected slices y existrvendoonlyinedes no True if RV endocardium exists in ED and ES slices y existrvepionlyinedes no True if RV epicardium exists in ED and ES slices 15 4 3 Input Output unit This unit consits of functions that are internal helper functions in Segment Interactions Interactions are minimal Datastructure Not applicable 113 CHAPTER 15 UNIT IMPLEMENTATION Functions 15 4 4 myadjust m MYADJUST objecthandle and fighandle mygui object Adjust so that a message box gets to the correct screen fighandle is a figure handle 15 4 5 mybrowser m MYBROWSER URL Opens an URL platform independent 15 4 6 myclientserver m MYCLIENTSERVER Class to create interface object to communicate with a computational server that can perform tasks in background B MYCLIENTSERVER NAME Sets up a comp
21. 15 8 Tools superunit 15 9 File superunit vos 2 2 dee ee dua 15 9 1 Open File unit 15 9 2 Image file reader unit 15 9 3 DICOM file write unit 15 9 4 Database unit 15 9 5 PACS DMA 2 4s vs e eee oo x 15 9 6 Segment Server unit 15 9 7 File menu unditl 15 9 8 Utility unit lt 2 42 ce teen 15 9 9 Sectra A 15 9 10 External PACS unit 15 10 Analysis superunit 15 10 1 T2 unit o ee ee ee ee 15 10 2 Perfusion unit oa aaa aa 15 10 3 Strain unit 204 lt 4 va eee am lt 15 10 4 Strain tagging unit 15 10 5 MPR unit sisi 15 10 6 Fusion unit oaa aaa 15 10 7 General segmentation unit 16 Module Implementation 16 1 Brukermodulel 16 1 1 Interactions 16 1 2 Datastructurel 16 1 3 Functions 0 16 2 MIP module 16 2 1 Interactions 16 2 2 Datastructurel 16 2 3 Functions 0 16 3 Corelab module 16 3 1 Interactions 16 3 2 Datastructure 2 16 3 3 Functions 0 17 Testing Segment 17 1 Testing functionality 17 2 How to write testcases in maketest m vil CONTENTS 17 2 1 Writing test function 17 2 2 Add test function to list of tests 17 3
22. Chapter 11 Interactions Superunits called from the main Segment unit are e Draw Graphical updates upon commands to change view or modify an image e Calc Calculations for images or quantifications that are used in the GUI Datastructure The data structure is the previously described SET structure and the DATA object Functions in segment _main m addtopanels no mode Finds an open space otherwise increases number of panels addviewicon_helper callback tooltip cdata tag separator Helper fcn to add an icon 75 CHAPTER 15 UNIT IMPLEMENTATION x y name askcontour queststri Show menu so that user can indicate what contour to use Used by levelset to import contours and by export function to export contours as ascii file returns contour in x and y and a name of the contour autocontrast no Helper functionk to autocontrast_Callback_ autocontrast_Callback Automatically calculates contrast settings autolongaxis_Callback Callback for automated long axis dectection mode varargout cell2clipboard outdata writetofile Converts a cell to a string that is output to clipboard If more than 8000 cells are written then an xls file is written instead Note that this used active X on Windows and requires Excel to be installed on the computer center_Buttondown panel Called when center is pressed down sets motion and buttonup fcns center_Buttonup This function is called when buttonup occurs aft
23. IMPLEMENTATION result updateintersections_Callback slices no type Calculates the intersection of a endocardial segmentation and SET no for slices all or slices current Allowed segmenation type is LVEndo or RVEndo Calculates intersection for SET NO if nargin 1 Returns false if calculations fails updatemmode arg nbrofcycles Calculate and show mmode image updatemmodeline Updates the mmode line in mmode display updatemmodevisibility Updates mmode visibility updatemodeldisplay Do nothing introduced to disable excessive calls to updatemodeldisplay updateoneim no Updates viewim for one view or mmodespatial Called when changed currentslice updateparallelsets Chages CurrentSlice in SETs that are parallel to SET NO to the slice closest to SET NO CurrentSlice Help function to movealltowardsbase _Callback and movealltowardsapex_Callback updateselectedslices Graphically updates which slices are selected updateslider whattodo Update when user changes in thumbnail slider 88 15 1 MAIN SEGMENT SUPERUNIT updateviewicons no Enables Disables icons depending on image data nbr timeframes etc updatevolume lvsegchanged Calc volume of segmentation and graphically update userlongaxis_Callback Callback to set user adjusted long axis motion viewaddtoolbar_Callback Helper function to add a toolbar viewallimagestacks_Callback Displays al
24. Interactions Calls to other superunits are negligible Datastructure The calculation tools uses the SET struct and sometimes also use the global variable NO for indicating current image stack Functions bsa calcbsa weight height Calculates BSA Formula based on Mosteller weight in kilo and height in cm calcdatasetpreview Calculate thumbnails They are stored in the variable DATA DATASETPREVIEW Size of the thumbnails is given by DATA GUISettings ThumbnailSize It is stored as a RGB image 105 CHAPTER 15 UNIT IMPLEMENTATION rad calcendoradius no Calculates endocardial radius Respects setting in preferences if to use endocardial or epicardial center as reference Loops over timeframes and slices rad calcepiradius no Calculates epicardial radius Respects setting if to use endocardial or epicardial center in calculation Loops over timeframes and slices meanint defectextent varargout calcintensityanddefect im tf numpoints numsectors nprofiles pos no endox endoy epix epiy sz resolution defect numwidth Calculates the mean intensity within sectors as a preperation to generate a bullseye plot numsectors number of sectors nprofiles number of profiles pos slices to use endox endoy epix epiy myocardial borders SZ size of image stack resolution resolution of image stack varargout calclvvolume no docomp Calculate LV volume Docomp if to use longaxis motion see below Uses area th
25. Johannes T ger 3D flow and volume tracking Marten Larsson 3D flow and kinetic energy Commercial development has been done by Jane Sj gren improvements to general object segmentation implementation of prototype based segmenta tion CT functionality and graphical seriesselector General debugging and implementation of the new interpolated contours has been done by Johan Ugander and Erik S dervall Report Module and general debugging have been performed by Nils Lundahl 4 Conventions and Abbreviations This chapter describes the typographic conventions and used abbreviations in this manual and in the program 4 1 Typographic conventions A Key A at the keyboard Ctrl A Control key Hold down Ctrl key and A simultaneously po Icon in toolbar mat Filename extension C Program Folder File Menu e g File menu File gt Save As Sub menu e g under the File menu the item Save As is found Close Push Toggle button in the graphical user interface Endocardium Radiobutton in the graphical user interface X Single frame Checkbox in the graphical user interface 4 2 Trademarks Below are some of the trademarks used in this manual e Segment is a trademark of Medviso AB e Segment DICOM Server is a trademark of Medviso AB e Sectra PACS is a trademark of Sectra Imtec AB http www sectra se e Matlab is a trademark of the Mathworks Inc http www mathworks com 4 3 Abbreviations 2CH Two
26. PACS connection unit uses slaves that operates as different processes for the actual retreival and then in a loop checks that all the files have been received and updates the waitbars as appropriate This usage of slaves is to prevent Segment to just go into a sleep mode while retrieving since we use DCMTK binaries for the recieve operations This also have the ad vantage of splitting the work over multiple cores if available The commu nication between the slaves are performed by inbox files and outbox files These inbox files are stored in the same folder as where the preferences are stored The underlying client server functions are implemented in the class myclientserver m The communication is as ordinary ascii files and the protocol is defined in encodemessage m and decodemessage m The actual work is performed by a compiled function called slave Adding studies to the patient database is done by calling the function patientdatabaseaddstudyhelper m 15 9 6 Segment Server unit The Segment Server unit is a standalone software that turns the computer into a DICOM server that can receive image data directly from an MR scan ner 200 15 9 FILE SUPERUNIT Interactions This unit interacts with the Database unit to add received studies to the patient database Datastructure The DATA variable is used to extract network options The unit also uses its own global variable SERVER to keep track of its state Functions Functions are
27. Segmentation Stores information related to the parameters in the level set segmentation View Stores information related to the graphical viewing of the seg mentation Pen Stores information related to the pen used for manual segmenta tion Prototype Stores information related to prototype based segmenta tion using level set RegionGrowing Stores information related to region growing segmen tation using level set The most important subfields of DATA LevelSet are 230 BackupBWInd Stores the indices of SET LevelSet BW from previous segmentation iteration to be able to go back to previous iteration BackupManAddInd Stores the positive indices of SET LevelSet Man from previous segmentation iteration to be able to go back to previous iteration BackupManRemovelInd Stores the negative indices of SET LevelSet Man from previous segmentation iteration to be able to go back to previous iteration SpeedIM Stores the speed image calculated from SET LevelSet Speed GradientPart Stores the gradient calculated from SET IM 15 10 ANALYSIS SUPERUNIT e Protototype Stores information related to prototype based segmen tation which does not need to be saved in SET LevelSet Prototype Functions all functions relevant for the unit is implemented in levelset m 231 16 Module Implementation 16 1 Bruker module The documentation for the usage of the Bruker Module is given in Segment User Manual 16 1 1 Interactions The m
28. a time and attempts to merge them loadfiles dicomfiles showprogress cropbox Load files loadmultidataset setstruct Load mat file Sets up display and exits GUI and return back to segment loadpreview Loads a preview of the function takes a filename or a pathname loadpushbutton_Callback This function is called when user press load ote that the function only works for non time resolved images Are you sure you want to continue Uturn pathlistbox_Callback updir This function is called when user selects something in the file dir selection listbox If called with on input variable then go up one directory level plotslicelocation_Callback Plots graphical display of slicelocation of DICOM files refresh_Callback Refresh GUI roisizelistbox_Callback insize Callback for ROI size selection selectall_Callback Select all files callback 182 15 9 FILE SUPERUNIT setimagetype_Callback Set image type callback setimageviewplane_Callback Set image type callback setimagingtechnique_Callback Set imaging technique callback setupstacksfromdicom no This function is called when managed to load an image volume from DICOM files It is essential for enabling and setting up things setupstacksfrommat no This function is called when managed to load an image volume from mat files It is essential for enabling and setting up things updir_Callback Fake a double click on 15 9 2 Imag
29. algorithm see 11 for details e Percentage a scalar representing the percentage of the pixels that are marked as infarcted e OnlyEndo true if only endocardium delineation exists e UseWeighting true if weighted mode is used e MOPercentage percentage microvascular obstruction e UpdateDirectly true if direct update on volumes should be performed after adjustments e minweight this is the minimal weight used in the weighting algorithm e MOThreshold threshold used for microvascular obstruction The MO threshold is defined as threshold for myocardium times MOThreshold Functions patchinessindex fullindex calcpatchinessindex no Calculates a patchiness index Roughtly it is the perimeter of the scar divided with twice the length of the scar res varargout calctransmuralityline numsectors no Calculates transmurality Output in order Mean transmurality in the number of sectors Max transmurality in each sector 158 15 6 SEGMENTATION SUPERUNIT Mean transmurality calculated only over infarcted areas Total Extent Start transmurality End transmurality Note that you need to set StartSlice and EndSlice res varargout calctransmuralityweighted numsectors no Calculate transmurality according to the weighted method core greyzone scarregion calcweightedgreyzone no Calculates greyzone according to weighted method grayzoneclear_Callback Removes Gray Zone analysis from current imag
30. and regional wall motion analysis If false the the center of the epicardial surface is used e BlackWhite True if the lines contours should be drawn in white color instead of object specific colors e LineWidth Width of the lines Default is 1 e NumPoints Number of points to evaluate the endocontour along e LearnMode True if learning messages should be displayed 169 CHAPTER 15 UNIT IMPLEMENTATION e UndoHistory The maximum length of the undo history e reportsheetpath Path to where the files for the report sheets are generated e IncludeAl1PixelsInRoi If true then also pixels that are touched by the ROI are included in the subsequent processing Default is false and in this mode only pixels whose centrum are inside the contour are included e AutoSave If true then the segmentation is autosaved every fifth minute under the name autosave seg e ContourAdjustDistance The maximum distance to a contour a user can click before the contour is not acknowledged as a click on that contour Measured in pixels e PacsTempStoragePath The path where the temporary files for the PACS retreival are stored This field might be obsoleted in future versions e ExcludePapilars True if the papilars should be excluded in the au tomatic segmentation See Reference Manual and 2 3 for details e UseLight True if to use current brightness and contrast as a cue in the Segmentation process For further details see the Refer
31. coordinate system to RL AP FH coordinate system 15 4 Helper functions superunit This superunit contains functions that are frequently used to provide other functions with basic information about the state of Segment 15 4 1 Find unit The purpose of the Find unit is to contain functions that assist other func tions in finding requested image stacks or slices Interactions Calls to other superunits are negligible Datastructure The Find unit tools use the SET struct to look for information that is relevant to determining stack slice content 110 15 4 HELPER FUNCTIONS SUPERUNIT Functions cineshortaxisno findcineshortaxisno multiple Find only one cine short axis stack tfs findframeswithsegmentation type no Find timeframes in no containing segmentation of type x y findlvcenter no slices y 9 Finds the center of the LV uses the autocrop function as a helper function marno findmarshortaxisno Find only one mar shortaxis stack cineno scarno flowno strainno marno varargout findno Find matching image stacks output normalno normal short axis stack or closest equivalent scarno viability short axis stacks flowno flow image stack s marno stacks with MaR stress stress images Note that all scarno for instance is not garanteed to have non empty SET Scar scarno findscarshortaxisno Find only one scar shortaxis stack ind findslicewithendo no Find slices with endocard in any time
32. data table Also returns an indication of whether a value is outside the range of the reference gensvar_Callback This callback opens a GUI for sending report entries to Gensvar gensvarcancel_Callback Callback for cancel of sending report entries to Gensvar gensvarok_Callback Callback to approve sending of report entries to Gensvar gensvarpasswordedit_KeyPress hObject eventdata Callback activated when changing Gensvar password image_Callback imagetype Callback from image checkboxes all of them init Initialize GUI initreferencelistbox modality Initiates listbox of reference values lvanalysis_Callback Callback from LV analysis checkbox maranalysis_Callback Callback from MaR analysis checkbox perfusion_Callback Callback from perfusion analysis checkbox reset_Callback Sets all checkboxes to false and empties text edits reinserts template 143 CHAPTER 15 UNIT IMPLEMENTATION resetall_ Callback Resets the entire report rvanalysis_Callback Callback from RV analysis checkbox scaranalysis_Callback Callback from scar analysis checkbox screenshot_Callback Callback from screenshot checkbox sendtopacs_Callback Callback for making a report saving it as a DICOM and sending it to PACS shuntvalve_Callback Callback from Shunt and Valve analysis checkbox t2star_Callback Callback from T2 analysis checkbox textedit_Callback Callback from comments textedit update Update SET struct
33. directory and exports data on patient info and file location init Initialize utilitymenu called upon starting of Segment Calls private initialization method which adds private utilities for Medviso AB and Lund Cardiac MR Group marexport_Callback Export mar in 17 segment model nfound line numexist outdata rows name id Helper function to findindicomfiles scarexport_Callback Export scar in 17 segment model utilityanonymizemultiple_Callback pathname type Anonymize multiple datasets from mat files in a folder 203 CHAPTER 15 UNIT IMPLEMENTATION utilitycopyandsortfromcd_Callback Utility function to copy and sort files from CD Uses helper function dicomsorter to do the work utilitygrayzone Add grayzone utilities utilitygrayzoneexport Export grayzone analysis values utilitygrayzonesliceexport Export grayzone analysis values for each slice 15 9 9 Sectra unit The Sectra unit contains the Segment side implementation of the Sectra PACS plugin It consists of a timed function that repeatedly checks for in coming data from a Sectra PACS system once every second This is started in the function sectra m Sectra Process On the sectra side there is a code called segment segmentplugin32 d11 or segmentplugin64 d11 that is upon starting the Sectra interface is loaded and associated with the process Once the user clicks on Clinical applica tions and Segment then the code is invoked The first thin
34. files i e files named plugin xxx m Depending files is handled automatically since each plugin should respond which depending files For more information see wiki plugins C files Here you list all required c files i e MEX files The files are assumed to be compiled for each target platform See also makemex m Files to protect Here you list all files that should be protected and only be included in the source code format as precompiled p code Modules to include Each time you add a new m file to the Segment project you need to add it in makeit m either in the sections above or or as a module if the file is only used within a specific module The difference between adding it as a general m file or as a part of a module is readibility to enhance the understanding which m file belongs to which modules Generally modules should be the same as the modules listed in the file getmodule m Making a new module should be fairly straight forward by copy and past in makeit m 18 4 Multi platform support Currently Segment does not support multi platform except when running from Matlab Therefore compiling to standalone does only work for the Windows platform Things to fix before the compilation is supported for other platforms are e Changes not to generate a self extracting executable e Create and upload new MCR Installer package for each target platform 239 CHAPTER 18 COMPILING SEGMENT Note that there are also features t
35. hassegmentdata self Returns true if the tag SegmentData is present r hastriggertime self Returns true if has trigger time information r hasvelocityencodescale self Returns true if VelocityEncodeScale field is set r ignoreme self Returns true if this image should be ignored from the loading process 189 CHAPTER 15 UNIT IMPLEMENTATION r isduplicate self other Checks if other is the same as self r parsefloatstr data Parses a string with a number as a number of type double r parsesingle data Parses a uint8 matrix with four elements as a single number of type single timenum parsetime timestr Parse a dicom time string as number of seconds r parseuint16 data Parses a uint8 matrix with two elements as a single uint16 number dicoms readfiles files Returns a matrix of segdicomtags objects contaion DICOM info from files s ind removechars stri Removes everything except numbers and from a string self segdicomtags tags Constructor Sets the tags property r spacetimepos self returns the spacetimepos of the images switchtags self Switch to new tags r unpack self Unpack data from dicom file tags2find unpackhelper tags2find nested2find sequence explicit Helper function to unpack data EH 190 15 9 FILE SUPERUNIT Functions in segrawstack m r checkifcommon self method Calls method for all dicom files in the
36. image is seldom constructed e MagnitudeNo contains reference to which im age stack contains the magnitude informa tion For the image stack containing the magnitude information this points to itself e PhaseNo contains reference to the image stack containing the through plane flow in formation Naming is somewhat inconse quent by kept for legacy reasons A better name would be PhaseZ e PhaseX contains reference to the image stack containing the flow in the X direction Seg ment coordinate system e PhaseY contains reference to the image stack containing the flow in the Y direction Seg ment coordinate system Fusion Then there are also a few fields that are optional and only available when eddy current compensa tion has been performed These fields are PhaseCorr contains the phase offset for the current direction i e if the current image stack is velocity phase in the X direction then PhaseCorr contains phase offset in the X direction and so fourth This field is al ways present and if not applicable only an empty matrix is stored PhaseCorrPercentiles level of which per centiles to include in the detection of the static tissue See documentation on the eddy current compensation for further details PhaseCorrMethod contains the selected method for the eddy current compensation PhaseCorrTimeResolved true if the eddy current compensation is time resolved De fault value is false If time resolved
37. let user decide what data to be analysed in the histogram Also let s user decide how many bins in the histogram and if zero should be excluded values roihistogram_helper rois timeframes normalized excludezero export Helper function to roihistogram extracts values roiimportroi_Callback no Import roi from image stack Let s user select from which image in an input dialog roilabel_Callback x y Function for putting name on a roi roiputroi_Buttondown panel Buttondown function for putting circular roi roi roireset no Reset ROI values when stack is emptied rois timeframes normalized roiselector usealltimes thissliceonly template normalized Dialogbox in which user decides if all timeframes only this slice and normalized intensity values should be used All values can be changed seperately roisetcolor_Callback n Change color of roi Which roi to use is either decided by closest roi from clicked coordinate if input argument is 1 else by user selecting from a pick list roisetlabel_Callback n Change name of roi Which roi to use is either decided by closest roi from clicked coordinate if input argument is 1 else by user selecting from a pick list roiswitchsign_Callback m Switch sign of roi The sign is used when calcualting flow through roi 166 15 7 RESOURCES SUPERUNIT roitemplatedelete_Callback Function to delete roi by template roitemplatesetcolor_Callback Function to rename roi by te
38. mode mmodetemporal shows the temporal part of a mmode image display e mode mmodespatial shows the spatial part of a mmode image display The best way of changing viewing mode is to call the function viewimage Callback A cell array where each element i a two element vector containing the number of rows and columns for a montage view in the corresponding panel ViewIM ViewMatrix LastView CurrentPanel A cell array with the length same as ViewPanels Each element contains a uint8 array of size N x M x T where T is the number of time frames N and M are arbitrary numbers that depends on ViewPanelsType This is used for graphical out put and contains mapped intensities A two element vector with the size of the image panels n x m Save view settings for the last panel view Used upon double clicking to go from the current panel view to the last panel view Points to the current image panel This number needs to be in the range 1 N where N is the number of valid panels 35 CHAPTER 12 DATA OBJECT CurrentTool String containing the current tool Valid tools are e point e measure e select e dragendo e dragepi e drawendo e drawepi e drawrvendo e drawrvepi e drawroi e drawscar e drawrubber e drawrubberpen e endopin e epipin e contrast e crop CurrentTheme Indicates which set of segmentation tools is cur rently on display to the user Tools Structure of handles to tools available in the too
39. open source rules do apply Segment is a commercial product and is provided free of charge to the research community as a service and without any associated rights Medviso AB does not give you any rights to do commercial derivative works of it It does not give you the right to compile it to a distributable standalone form See discussion on license terms in El 3 Acknowledgements Even if this project started as a one man project it has grown and it would never been possible without the help of many many people Financial support has been received from the Swedish Heart Lung founda tion Swedish Research Council local founds from Osterg tland County and Region of Scania I would like to acknowledge all the people that have put in feed back on usability and desired functionality algorithm etc Among others Andreas Otto Andreas Sigfridsson Erik Bergvall Erik Hedstrom Henrik Haraldsson Henrik Engblom Hakan Arheden Jan Engvall Lars Wigstr m Lisa Hard af Segerstad Karin Markenroth Bloch Marcus Carlsson Martin Ugander Mikael Kanski Finally thank to you all Segment users in the research com munity that has inspired and contributed to the development Special thanks to code providers Erik Bergvall core routines of strain anal ysis Helen Soneson strain analysis module SPECT module Image fusion module Shruti Agarwal refactory of strain analysis module Jonatan Wul can Sectra Plugin module and general improvements
40. selection of regional restriction myocardium roi or full image resultpoint_Buttondown User clicked on image gives show fit resultpoint_Motion Motion function for dragging resultpoint in image smoothedit_Callback Callback for edit box of smoothing factor smoothslider_Callback Callback for slider to set smoothing factor smooththresedit_Callback Callback for edit box of smoothing error threshold smooththresslider_Callback Callback for slider to set smoothing error threshold smoothupdate Updates after smooth changes startline Buttondown Buttondown function for line indicating start of time period to fit startline Buttonup Buttonup function for line indicating start of time period to fit 209 CHAPTER 15 UNIT IMPLEMENTATION startline Motion Motion function for line indicating start of time period to fit thresedit Callback Callback for edit box of mag threshold thresslider_Callback Callback for slider to select threshold update_Callback Update everything updatefit Update the pixel wise fit display updateimage Update view of image updatemap Updates the map in the top right corner 15 10 2 Perfusion unit The purpose of the Perfusion unit is to provide tools for myocardial perfu sion analysis including rotation registration and extracting curves of signal intensity over time for quantification of upslopes to compare between rest and stress image stacks Interactions The C
41. then PhaseCorr has the same image dimensions as IM otherwise the third image dimension is one PhaseCorrStaticTissueRois true if regions where static tissue should be taken from drawn ROIs instead of estimated from the image Default value is false VelMag contains a reference to the image stack that contains a velocity magnitude stack absolute value of the velocity Nor mally this field is set to an empty vector as the velocity magnitude is seldom con structed Struct reserved for Fusion Module 51 CHAPTER 13 SET VARIABLE GEVENCSCALE HeartRate 52 IM ImageOrientation ImagePosition Special tag read from DICOM for GE scanners Hear rate of the image stack Note that different image stacks may have different heart rates Unit is beats per minute HeartRate is used to calculate cardiac output This field contains the image data stored as a 4D single array The order of the dimensions are X x Y x T x Z For more details on coordinate sys tem conventions see Section The image data should lie between 0 1 For more details on im age scaling see the fields IntensityScaling and IntensityOffset Same as DICOM tag Image0rientation If not presented then set to1 0 0 0 1 0 The three first numbers contains the normalized vector of Seg ments Y direction given in the patient table co ordinate system The last three numbers contains the direction of the X direction For further details on coordinate systems
42. viewimagestackas_Callback mode Select how to view current image stack viewinterp_Callback val viewmanualinteraction_Callback Displays a GUI indicating in which slices and timeframes manual interaction have been made for LV segmentation 90 15 1 MAIN SEGMENT SUPERUNIT viewpandir_Callback direction Pans current view panel viewrefresh_Callback Main graphical refresh viewrefreshall_Callback Main refresh of GUI viewspecial Callback mode Called to switch to predefined layouts of the GUI Mode is current mode to use viewzoomin_Callback Zooms in current view panel viewzoomout_Callback Zooms out in current view panel volumeaxes_Buttondown Called when user has clicked volume graph sets current timeframe to clicked point zoomhelper ax f no panel Helper function to zoom image stacks Zooming is done by changing xlim and ylin Functions in maingui m addmainicon_helper g callback tooltip cdata tag separator Helper function to add an icon checkversion g Check if new version is available Define separately for each GUI cleardatalevelset g onlyprototype Clear the struct g LevelSet properly called when switching image stacks contextmenu g Context menu button down callback Overloaded in CVQgui Note Can act on one slice CurrentSlice or range of slices StartSlice EndSlice 91 CHAPTER 15 UNIT IMPLEMENTATION copyrvendoforward Overloaded in SegmentGUI defaultpref g Sets Pref
43. 15 4 33 mystubfailed m Displays generic error message from stubs 15 4 34 myuigetdir m PATHNAME OK MYUIGETDIR PATHNAME TITLESTRI Corresponding to uigetdir but also fixes macro recording and test scripts 15 4 35 myuigetfile m FILENAME PATHNAME FILTERINDEX OK MYUIGETFILE FILTERSPEC TITLE Corresponding to uigetfile but also fixes macro recording and test scripts 15 4 36 myuiputfile m FILENAME PATHNAME FILTERINDEX OK MYUIPUTFILE FILTERSPEC TITLE Corresponding to uiputfile but also fixes macro recording and test scripts 121 CHAPTER 15 UNIT IMPLEMENTATION 15 4 37 myurlread m S URLREAD URL timeout reads the content at a URL into a string S If t server returns binary data the string will contain garbage S URLREAD URL timeout method PARAMS passes information to the serv part of the request The method can be get or post and PARAMS is cell array of param value pairs S STATUS URLREAD catches any errors and returns 1 if the file downloaded successfully and O otherwise Same as URLREAD except that it adds two timeout settings 15 4 38 mywaitbarclose m MYWAITBARCLOSE Closes a mywaitbar structure and removes waitbar See also MYWAITBARSTART MYWAITBARUPDATE 15 4 39 mywaitbarmainclose m MYWAITBARCLOSE Closes a mywaitbar structure and removes waitbar See also MYWAITBARSTART MYWAITBARUPDATE 15 4 40 mywaitbarmainstart m H
44. 2 15 10 ANALYSIS SUPERUNIT prevpushbutton_Callback field Callback for previous frame pushbutton for image specified by input parameter field rawalignedpanel SelectionChangeFcn hObject eventdata handles Selection change function for raw aligned radiobutton panel Currently not implemented rotatecheckbox_Callback Callback for checkbox toggling rotation mode rotatehandle ButtonUpFcn hObject rotobj midpoint field Buttonup function for handle used to rotate image specified by input parameter field Sets sector rotation and dectivates motion function rotatehandle_Buttondown hObject midpoint field Buttondown function for handle used to rotate image specified by input parameter field Activates motion function rotatehandle_MotionFen hObject rotobj midpoint field Motion function for handle used to rotate image specified by input parameter field Dragging rotates image settimeframe tag tf field Sets current start end timeframe for image stack specified by input parameter field sliceslider_Callback Callback of slider for toggling between slices in display smoothslider_Callback Callback of slider for changing smoothening factor Recalculates upslopes timebar ButtonDownFcn hObject field Buttondown function for graphical timebar object of image specified by input parameter field Activates dragging of timebars timebaraxes_ButtonDownFcn hObject field Button
45. 3 SET 1 Image0rientation 4 6 pos SET 1 ImagePosition 2 1 SET 1 ResolutionX SET 1 ImageOrientation 4 6 3 1 SET 1 ResolutionY SET 1 ImageOrientation 1 3 4 1 SET 1 SliceThickness SET 1 SliceGap zdir Coordinated conversions can be performed using the functions xyz2rlapfh and rlapfh2xyz in calcfunctions nm 20 8 Running Segment from Matlab You need to have Matlab R2011a or later to run Segment Running Seg ment from Matlab prompt is just as easy as running it as a stand alone application Note that necessary mex files have been compiled for Linux 64 bit and Windows both 64 and 32 bit When Matlab has started simply type gt gt segment To get acess to the internal variable direct from the Matlab prompt simply type gt gt global DATA SET NO To get the x coordinates of the endocardial segmentation in time frame 3 and slice 4 simply type gt gt x SET NO EndoX 3 4 To plot the segmentation in the current slice in another window type gt gt figure 22 plot SET NO EndoY SET NO CurrentTimeFrame SET NO CurrentSlice SET gt gt axis image off 21 9 Overview of Segment Segment is written in Matlab and is a fairly large software project Cur rently it contains of around 130 000 lines of m code distributed more than 200 files and 2815 subfunctions and 69 gui s There are 72 files c code with about 12 000 lines There are 22 su
46. 8 15 5 REPORT SUPERUNIT exportmultipleinfo_Callback Exports information of image stacks for a folder of mat files This function is useful for debugging and checking purposes of the integrity of multiple mat files exportrv2stl no tf fignr filename resolution Exports RV surface to STL with inner and outer contour closed in apex and surfaces merged in the base OBS this function ignores RV epicardium and fakes in an epicardium Wall thickness is set to 1mm exportrv2stl_Callback Exports RV to STL file This file ignores epicardium and fakes in a epicardium ok exportsavemovie mov left right up down fps Exports a move as an avi file or a set of png files mov is a movie struct left right up down are crop coordinates fps is frame rate Allows user to select different codecs outdata exportslicehelper outdata rowoffset coloffset type x y Helper function to export slice based data exportslicevolume_Callback Export slicebased volume exportthisstack doheader Export data from current image stack to clipboard exporttoclipboard_Callback doheader no Export data to clipboard Calls another function to do the export exporttoclipboardthisstack_Callback doheader Exports data for current image stack to clipboard exportvolumecurve_Callback Export volume curve to clipboard outdata ind header onlyone Helper function to write header when exporting data 149 CHAPTER 15 UNIT IMPLEMENTATION x
47. ARIABLE CurrentSlice CurrentTimeFrame Cyclic DICOMImageType EDT EDV EF EPV EST ESV EchoTime EndAnalysis 46 This field contains the current slice of the image volume This field contains the current time frame True for image stacks that are cyclic i e covers a complete heart cycle This flag is used by the seg mentation engine when delineating the left ventri cle This field contains the ImageType from the DI COM files Left ventricle end diastolic time Left ventricle end diastolic volume Left ventricle ejection fraction Volume inside the epicardial volume of the left ven tricle Left ventricle end systolic time Left ventricle end systolic volume Echo time in MRI pulse sequence Read from DI COM tags if presented otherwise set to zero Given in milliseconds End time of analysis used in flow quantification See also StartAnalysis For further details see Reference Manual for details Default value is same as TSize Endslice EndoCenter EndoDraged EndoInterpX EndoInterpxView EndoPinX EndoPinY EndoPinXView EndoPinYView This field contains the last slice in the set of selected slices The se lected slices is then given by ind SET NO StartSlice SET NO EndSlice The field may be an empty array when no slices are selected True if center of endocardium is used as center of the left ventricle when doing regional wall motion analysis If false t
48. CHAPTER 15 UNIT IMPLEMENTATION interpdeletepointall Delete interp points for all slices timeframes interpdeletepointthisslice Delete interp points this slice interpdeletepointthisslicephase Delete interp points this slice and phase interpdrawGuessPoints_Callback type panel Guess points in current selection then moves to corrosponding tool interpdraw_Buttondown panel type forcedraw Button down function to draw interp points interpx interpy interpdrawhelper interpx interpy contourx contoury x y Helper fcn to interpdrawbuttonup Side effects is update of DATA Pin xout yout interphelper pinx piny Interpolates points to create a contour without loops interppointButtonup type Button up function for interp points interppointMotion type Motion function for interp points tool interptoolfromcoords x y slice get tool from point valid for interpendo interpepi interprvendo interprvepi mainresize_Callback This fcn is called when user resizes GUI makeviewim panel no Rearrange data to show all slices manualdraw_Buttondown panel type new Button down function for manual drawings 80 15 1 MAIN SEGMENT SUPERUNIT manualdraw_Buttonup type new obj Button up function for manual drawing manualdraw_Motion Motion function for manual drawings mccheckconsistency Check consistency to prevent earlier manual segmentations that have problems with direction left right
49. Callback g arg Rename current measurement Overloaded in CVQgui mywaitbarclose h Makes it possible to overload mywaitbar behaviour h mywaitbarstart iter stri ignorelimit fighandle Makes it possible to overload the mywaitbarstart behaviour h mywaitbarupdate h Makes it possible to overload mywaitbar behaviour 94 15 1 MAIN SEGMENT SUPERUNIT normalizephaseupdate g Called by segpref m methods Overloaded in CVQgui different handle placement plotrois g panel no Plot roi s if existing Overloaded in CVQgui point_Buttondown g panel Button down function when point tool is active Overloaded in CVQgui pointshowthisframeonly_Callback Callback to make the current point visible in this time frame only Overloaded in CVQgui printthumbnailnumber g thumbsize Overloaded in RVQ GUI really quit g Quit segment also ask user if he she is sure Overloaded in CVQgui renderstacksfrommat g This function displays stacks from a mat files in main gui Typically called upon loading name roilabelmenu g roitoname roinamein Prompt name of ROI from a menu selection Overloaded in CVQ and RVQ roiputroi_helper g no m Called by roi roiputroi _Buttondown Overloaded in CVQgui and RVQgui segmentclearall_Callback g force Clear all segmentation both endo and epi lv and rv Overloaded in CVQgui and RVQgui segmentclearallbutsystolediastole_Callback g Clears all segmentation in all timefram
50. E y ie in aii December 11 2015 Software platform v2 0 R4790 MEDVISO AB http www medviso com Griffelvagen 3 SE 224 67 Lund Sweden Tel 46 76 183 6442 Contents 1 Regulatory status 1 1 Commercial usage of Segment 12 Indications for use 1 3 Investigational purposes o 2 License terms 3 Acknowledgements 4 Conventions and Abbreviations 4 1 Typographic conventions 5 24 55 8 ee bee eee es 4 2 Trademarks 4 3 Abbreviations 5 Document purpose 6 Coding Conventions 6 1 Naming functions 6 2 Naming variables 6 3 Name graphical handles lt i us ewe ee eee aS 6 4 Object oriented programming 6 5 Packaging 6 6 General coding conventions 04 67 Units 6 8 Graphical user interfaces 6 9 Indentation and spacing 4 6 10 Documenting code 11 13 13 13 14 14 15 15 15 15 16 16 iii CONTENTS 19 7 1 Introduction 0 0 0 0 0 0 0 000000084 19 8 Running Segment from Matlab 21 23 25 LARA A RA 26 10 2 OTS software and SOUP elements 26 Oe EE a a a 26 10 2 2 SOUP elements 27 10 3 Protected code sections 2 2 4 2 28 Ao a ae 29 31 11 1 General class hierarchy 31 11 2 Compilation class hierarchy 31 12 DATA Obj
51. HA 17 segment model m is a matrix in polar coordinates It could also be a vector of 17 segments Please note in such cases then the order is not the same as the standard AHA numbering The names are given by the function ahal nameandpos ax is axis to plot it in n is the number of pixels valuetype is how to treat the merging of data into sectors mean sum max bullseyelistbox_Callback Callback for bullseye listbox Updates plot 132 15 5 REPORT SUPERUNIT close_Callback Properly close the GUI colormaplistbox_Callback Callback for colormap listbox Updates plot defineslices sign part drawsectorimage Draw image of sector division in new figure endocenter Called when the endocenter checkbox is clicked Updates SET EndoCenter varargout export Export data to clipboard value getdata type Helper function to extract data from the module Used for instance from reportsheet generator init Initialize the GUI initlaximage invertcolors_Callback Callback for invert colors checkbox Updates plot maxedit_Callback Callback for edit to change max value Updates plot minedit_Callback Callback for edit to change min value Updates plot nedit_Callback Callback for edit to change value of n Updates plot plotmethodpanel SelectionChange Callback for changing type of plot sector smooth or AHA model 133 CHAPTER 15 UNIT IMPLEMENTATION rotationfromannotation_Callback Finds rotation
52. MYWAITBARSTART NUMITERATIONS STRING IGNORELIMIT FIGHANDLE Similar to waitbar but first input argument is the total number of iterations that will be performed Second input argument is string that will be displayed and third optional argument is a limit that if fewer iterations that this is performed then there will be no graphical output Another difference to standard waitbar 122 15 4 HELPER FUNCTIONS SUPERUNIT is that no more than 20 graphical steps are displayed to minimize CPU consumption Function returns a handle to a MYWAITBAROBJECT FIGHANDLE is optional and indicates alignment See also MYWAITBARUPDATE MYWAITBARCLOSE 15 4 41 mywaitbarmainupdate m H MYWAITBARDATE H Update a mywaitbarstructure and increment counter one step Graphic is updated depends on setting when intializing the structure See also MYWAITBARSTART MYWAITBARCLOSE 15 4 42 mywaitbarstart m H MYWAITBARSTART NUMITERATIONS STRING IGNORELIMIT FIGHANDLE Similar to waitbar but first input argument is the total number of iterations that will be performed Second input argument is string that will be displayed and third optional argument is a limit that if fewer iterations that this is performed then there will be no graphical output Another difference to standard waitbar is that no more than 20 graphical steps are displayed to minimize CPU consumption Function returns a handle to a MYWAITBAROBJECT FIGHANDLE is opti
53. Manually entered or automatically calcu lated from Weight and Length See Refer ence manual for details and equations used e Weight Measured in kilograms Applied values are 0 or numeric value e Length Measured in centimeters Applied values are 0 or numeric value This is a struct containing information for perfu sion analysis Struct that contains data of annotation points Please see Section 15 6 2 for details Describes the version of which the set struct was created Used for backwards compability issues and also to detect potential forward compability issues Right ventricle end diastolic volume see also EDV RVEF RVEPV RVESV RVEndoInterpxX RVEndoInterpxView RVEndoInterpY RVEndoInterpYView RVEndoX RVEndoXView RVEndoY RVEndoYView RVEpiInterpx RVEpiInterpxView RVEpi InterpY RVEpiInterpYView RVEpiPinX RVEpiPinXView RVEpiPinY Right ventricle ejection fraction see also EF Right ventricle epicardial volume see also EPV Right ventricle end systolic volume see also ESV RV interpolation points RV interpolation points RV interpolation points RV interpolation points Endocardial contour of the right ventricle See also EndoX Same as EndoXView but for the right ventricle en docardium See above See above RV epicardial interpolation points RV epicardial interpolation points RV epicardial interpolation points RV epicardial interpolation points RV epicardial interpol
54. N exportcontour_Callback Export contour Ask what contour to take varargout exportdata doheader includenormalized no This is the workhorse of export functions doheader tells whether to include a header includenormalized tells whether to include BSA normalized data no tells whether to export ONLY image stack no exportendoepitoensight_Callback Exports endocardium and epicardium in Ensight format exportimage_Callback image2store Export an image to an image file If no input image exist export current image w exportleftatria2stl no tf fignr filename resolution Exports RV epicardium surface to STL but names it LV atria Closed in base Wall thickness is set to 1mm exportlv2ensight_Callback Export left ventricle to Ensight exportlv2stl no tf fignr filename resolution Exports LV surface to STL with inner and outer contour closed in apex and surfaces merged in the base exportlv2stl_Callback Exports LV endo and epi as one surface and takes care of closing the surface suitable to read into CAD software exportmovie_Callback Function to export a movie without contours This is a quick method to generate a movie of the current image stack exportmovierecorder_Callback arg Movie recorder GUI exportmultiple_Callback dosegdicom Creaty summary of multiple matfiles in one folder This function is very useful for research The user performs all delineations and then exports all data to one spread sheet 14
55. NIT drawannotationpoints no panel Draw annotation points if available drawcolorbar panel Draw color bar in an image panel drawcontours no panel Initiate handles and draw endo and epicardial contours of the LV and RV drawcontrastimage no draws contrast image drawimagehlavla panel viashow marshow olshow Main workhorse for creating view of one image slice viashow is whether to show viability marshow is whether to show MaR olshow is whether to show overlays or not drawimagemmode no panel Draw temporal mmode view drawimagemontage panel viashow marshow Main workhorse for creating montage view viashow is if viability data should be updated marshow is if MaR data should be updated drawimageno no Call drawimagepanel for the panels that contain no including flow panels If no is not specified then the current image stack NO is used This function is typically called when new objects have been created or modified drawimageone panel viashow marshow olshow Main workhorse for creating view of one image slice viashow is whether to show viability marshow is whether to show MaR olshow is whether to show overlays or not drawimagepanel panel Draws selected panels used upon loading or when when major changes have occured such as change of slice added measurement points etc This fcn is the true workhorse in graphics etc 101 CHAPTER 15 UNIT IMPLEMENTATION drawimagetypetext no pno pane
56. ORT SUPERUNIT 15 5 11 Export unit The exporting tools exports data from the SET structure or mat files to the clipboard Interactions The functions in the Calculation superunit are used frequently and the func tion cell2clipboard from the Main superunit is used extensibly Datastructure The exporting routines use the SET structure Functions export2stl_Callback Exports mesh in current image stack as STL file Asks for surface to export and then takes current timeframe to export export2stl helper no x y resolution tf closeapex fignr pathname filename Helper function that fixes with coordinates etc before exporting exportall2stl no pathname filetemplate fignr resolution tf Helper function to exportall2stl exportall2stl_Callback Exports all contours and ROI s to stl file s LV endo and epi gives left ventricle RV endo gives right ventricle with imm thickness RV epi gives left atrium closed in base ROI s gives tubes with 1 mm thickness exportbatch2stl_Callback Export all2stl for multiple mat files exportclosesurfaces no1 x1 y1 n02 x2 y2 closebase closeapex resolution fignr fid Helper function to close to surfaces basal and export to STL file Please not that this takes a mesh in form of points slices i e timeframe already selected This is different from elsewere in STL export not and no2 are required to be able to calculate 3D coordinates patient system 147 CHAPTER 15 UNIT IMPLEMENTATIO
57. TATION viewnext_Callback User has clicked on next button Move to next time frame viewparameter_Callback Called when user adjusts colorscale or setting gui viewplay_Callback play a movie of strain over time viewplaypushbutton_Callback Start to play from pushbutton viewprev_Callback move to previus time frame viewtrackupdate Update the tracking graphically 15 10 4 Strain tagging unit The Strain tagging unit allows to calculate strain from tagging images Interactions The function interacts with the Helper function unit and the Calc unit Datastructure The module uses an own data structure in the field SET StrainTagging Functions analyse_Callback Do strain analysis calcpoints Calculate positions of points used for strain calculation close_Callback Close straintagging GUI 222 15 10 ANALYSIS SUPERUNIT hideanatomicalcontour_Callback Hide segmentation contours in anatomical image hidetaggingcontour_Callback Hide segmentation contours in tagging image hidetagginggrid_Callback Hide grid in tagging image hidetaggingpoints_Callback Hide points in tagging image importfromcine_Callback Import segmentation to tagging image from cine stack init Initialize the GUI inittimebar Initiate timebar axis makeslicemat From the current slice make mat file used by the executable makevtk Save tracking grid and points to vtk files used by the executable next Callback Callbac
58. ace acquisition scheme so for scanners that do not report TriggerTime you really need to double check the estimated value of time increment For perfusion and other image stacks with non uniform time increment this is calculated using differences in AcquisitionTime Heart rate The heart rate is taken from the DICOM tag HeartRate if present Note that many vendors including Siemens does not specify this As a fall back Segment tries to calculate the heart rate assum ing full R R intervall coverage by using of trigger time i e it does not working for prospective imaging series For long image acquisitions where one image is taken approximately for each heart beat then the heart rate is taken as the time between start of image acquisition and end of image acquisition adjusted for the number of frames Note that in many cases this heart rate calculation will fail Heart rate can be adjusted under patient details Note also that heart rate may vary be tween image stacks therefore do not press Apply for all when manually changing heart rate Heart rate is not used in any calculaion instead time increment between image frames is used in all calculations Slice thickness in mm The slice thickness is taken from the DICOM tag SliceThickness If this tag is not present then the information is taken from same DICOM tags as number of slices and assuming slice gap to be 0 Gap between slices in mm This is taken from the DICOM tag Spacing BetweenSlic
59. age view updatemontagepoints no panel Update coordinates of annotation point handles for montage view updatemontagerois no panel Update coordnates of ROI handles for montage view updatenopanels no Update panels containing image stack no updatepins no panel Update coordinates of pin handles updaterois no panel Update coordinates of ROI handles updatesax3contours no panel Update coordinates of contour handles for SAX3 image view updatevisibility Make sure visibility of handles correspond to status of hide show icons 104 15 3 CALCULATION SUPERUNIT viewupdateannotext panel Updates the visibility of point measurement text Respects hideX settings If point is inbound pointtext is visible If measurementtext is inbound measurementtext is visible If whole ROI is inbound place XXXX If only some of ROI is inbound place at any inbound point If whole ROI is outside make ROItext not visible viewupdatetextposition panel Updates the location of the corner text to always stay still From drawx it is called panelwise since the linked panels aren t ready when the first panel is drawn From other situations it is called without arguements and handles the linkage by itself JU 15 3 Calculation superunit The purpose of the calculation unit is to provide general functionality in the Segment platform This also prevents from code duplication of core functionality such as calculation of volumes
60. alance between the anatomical and functional images in the fusion imag transparent _Callback movement update the intensity balance between the anatomical and functional images in the fusion il undo_Callback undo the last translation or rotation update imagestack update all image stacks after left mouse click in the anatomical or functional image stacks updateanatomic update the anatomic image stack updatefunctional update the functional image stack updatefusion update the fusion image stack updatesegmentation update the segmentation and lines in all images 15 10 7 General segmentation unit The purpose of the general segmentation tool is to be able to do semi automatic segmentation of general objects and not only left ventricle and right ventricle The unit is based on using a level set method and the user can change many inputs to the levelset to get a good segmentation Interactions Interactions are negligible 229 CHAPTER 15 UNIT IMPLEMENTATION Datastructure Relevant data for general segmentation is stored in the field LevelSet in both the SET variable and the DATA variable The most important subfield of SET LevelSet are BW The resulting segmentation stored as 0 or 1 black or white Man The manual segmentation Object Stores information related to dividing the segmentation into seperate objects Speed Stores information related to the speed image used in the level set segmentation
61. alculation superunit is used to do calculations of slice positions inter sections and signal intensities by sector The Find unit from Helper functions is used to identify cine and scar image stacks Datastructure The image information on which to operate is taken from the SET struct The field Perfusion is used for storing the final quantifications of upslope comparisons 210 15 10 ANALYSIS SUPERUNIT Functions ScrollWheelFcn hObject eventdata Scroll wheel function of GUI Moves slider to toggle between slices bloodpoolcheckbox_Callback field Callback for checkbox toggling display of bloodpool curve and upslope smoothed t calcsmoothing curves tvec tups sigma Calculate smoothening tups time units per second calcupslopes Calculate upslope curves and draw plots and bullseye close_Callback Callback for closing GUI contourcheckbox_Callback Callback for checkbox toggling display of segmentation contours contractsegmentationpushbutton_Callback field Create ROI s defining contracted area of segmentation to be used if available instead of LV data curvepopupmenu_Callback Callback for changing sector to plot Update both curve plots drawbullseye ax txth perfvec Outline an AHA bullseye plot in axes with handle ax Also updates report text with handle txth drawimages field Do an update of all image axes drawlongaxisimage zslices Update axis containing longaxis image if available expo
62. alled for export of data Datastructure The regional function information is taken from the SET struct Number of stack to report is taken from the NO variable Functions close_Callback Close GUI export _Callback Export data to clipboard Renamed to avoid confusion with export m frac Callback upon changing frac wall radiobutton selection to frac frameupdate Different timeframe update less init Initiate GUI next Callback to go to next frame parameter Update things upon changed selection in parameter listbox play Callback for video playback prev Callback to go to previous frame 130 15 5 REPORT SUPERUNIT sector Update plots upon changed sector rotation sectors Update upon changing number of sectors slice Different slice update a lot of things update Update GUI wall Callback upon changing frac wall radiobutton selection to wall 15 5 6 Report Bullseye unit The purpose of the Bullseye unit is to be able to present quantifiable segmen tation parameters as bullseye plots Derived variables from LV segmentation viability can be presented To plot and not color the apical sector alphamap ping is used This requires a renderer that supports this alpha mapping The algorithm to convert to a 17 segment model is performed by replicating each slice into three separate slices with the slice thickness that is one third of the original slice thickness Then the total number of slices ar
63. anual seg mentation of the ischemic myocardium at risk from either MRI or SPECT Struct that contains data of measurements Please see Section 15 6 1 for details X coordinate for the center of the mmode line X coordinate for the center of the mmode line Direction coefficient of the mmode line Direction coefficient of the mmode line Distance from the mmode line center to the first measurement point Usually a positive value Distance from the mmode line center to the second measurement point Usually a negative value 57 CHAPTER 13 SET VARIABLE Modality Same as the corresponding DICOM tag MontageRowZoomState Four element vector describing the current zoom MontageZoomState Normal ZoomState NumberOfAverages OrgXSize OrigFileName Overlay PER PERT 98 state for the image stack in row montage view mode This representation is potentially subject to future changes Four element vector describing the current zoom state for the image stack in montage view mode This representation is potentially subject to future changes Four element vector describing the current zoom state for the image stack in normal mode This representation is potentially subject to future changes Number of averages acquired in MRI pulse se quence Read from DICOM tags if presented oth erwise set to zero This refers to the original X size of the images in the DICOM files This is used to load seg files to u
64. apex 83 CHAPTER 15 UNIT IMPLEMENTATION movetowardsbase_Callback Change current slice towards base nextallframe_Callback Displays next timeframe in currrent image panel and adjust all visiable image stacks to the corresponding part of the cardiac cycle nextframe_Callback Displays next timeframe of current image panel Sideeffect is that the movie display is stopped if running normal_Buttondown panel Called when button down in normal view sameview orientationcomparison setindex1 setindex2 Compares the SET ImageOrientation between two SETS Help function to updateparallelsets Return values sameview true if the orientations are parallel pan_Buttondown Button down function for panning of current image panel pan_Buttonup Button up function for panning pan_Motion init Motion function of pan pin_Buttonup Button up function for pins pin_Motion type Motion function for pins PinX PinY pinwarn pinresize PinX PinY tf slice mean f Helper function to move pins when resizing contours placetimeresolvedpoints_Callback When this option is enabled then points are placed timeresolved and the name is re used 84 15 1 MAIN SEGMENT SUPERUNIT playall_Callback keypress Starts movie display of all visible image stacks playmovie_Callback keypress Starts playing current image stack as a movie plotmodelrot_Callback daz del Changes view of 3D model of the segmentation x y pointsf
65. ath Generate an empty preview struct x y slice getclickedcoords Find coordinates where the user last clicked x and y are given in internal coordinate system i e the functions determines slice in montage view 78 15 1 MAIN SEGMENT SUPERUNIT no getclickedpreview y function which returns the clicked preview image intersections maxintersect getendointersection no Returns the intersection of the endocardial segmentation and the current slice and current time frame of SET no r getfieldifcommon SET fname Helper function to filesavedicom_Callback t getframenumber Calculates what frame to show when playing a movie if storing a movie then show next frame otherwise user timer info slicestoinclude getmontagesegmentedslices no Get slices to include in montage segmented view numericversion getnumericversion function called to get versionnumber after R For example in 1 9 R4040 this function re helpimagepos im sector ofs konst helper function to display image helpimageposneg im sector konst helper function to display image highlighttool h Helper function to change color of a tool to represent that the tool is selected fig initializesegment programversion Initialization of Segment GUI initmenu Initalize the main menu for instance adds extra utilities and plugins iconhandles initviewtoolbar Initalize view toolbar interpdeletepoint Delete interp point 79
66. ation points RV epicardial interpolation points RV epicardial interpolation points 61 CHAPTER 13 SET VARIABLE RVEpiPinYView RVEpiX RVEpiXView RVEpiY RVEpiYView RVM RVSV RVV RepetitionTime Report ResolutionX Roi RoiCurrent RoiN 62 RV epicardial interpolation points Epicardial contour of the right ventricle See also Epix Same as EpiXView but for the right ventricle en docardium See above See above Right ventricle mass see also LVM Right ventricle strove volume see also SV Right ventricle volume See LVV Repetition time in MRI pulse sequence Read from DICOM tags if presented otherwise set to zero Given in milliseconds Field used to contain information for the patient report sheet generator functionality This field is only set for the first image stack i e SET 1 The exact content of this struct is subject to change Contains pixelspace in mm in X direction For discussion on coordinate systems see Section ResolutionY gives pixelsize in mm in Y direction a struct that contains information of store region of interest ROI Please see Section 15 6 8 for details number of current Roi number of Rois in total in the image Rotated RotationCenter SV Scanner Scar SectorRotation SequenceName True for image stacks that are rotated around a common rotation axis This is currently imple mented as an add on and only affects the volume cal
67. ave the images they contain to self images settimes self dimsizes timeDist Set the self images spacetimepos 4 that is time coordiante according to timeDist and a certain sorting Functions in rotrawstack m dimsizes getdimensionsizes self cropbox Gets the size of each dimension i e number of frames depth x size y size r hascollisions self imbase offset Returns true if two images in the object gets the same coordinates using imbase and offset r ismatch self dicom Check if a dicom files has one of the lines in this stack base offset makeimbase self dimsizes Return a base for the loaded image stack 194 15 9 FILE SUPERUNIT im makeimdata self imbase offset dimsizes cropbox Combines all images in the stack to an im suitable for SET im r render self datapath cropbox Renders the dicom files and images in this stack to a preview and set struct suitable for passing on to segment m If cropbox load entire image self rotrawstack lines imaxis Constuctor Initiate all properties 15 9 3 DICOM file write unit Writing DICOM files from Segment is implemented by the class segdicomfile Interactions Interactions are limited to calling arguments from the class creator Datastructure No use of shared datastructures occurs Functions methods in segdicomfile m create filename data study_uid pat_name pat_id pat_birth pat_sex switchtags RCreats a dic
68. ble or scar is done on a pixel wise basis and there the volume calculations are done by summing the number of pixels For the rotated image stacks the volume is given by a integration method The volume contribution of each outline is given by Vv E uls sign uls Zas 3 where the curve is given on a parametric representation x s y s Z is the number of slices in the rotated image stack No long axis compensation is performed for the rotated image stacks 14 5 Mass calculations When converting volume to mass the density is assumed to be 1 05 g ml Note that this number differs in the literature between 1 04 to 1 05 Further more note that these numbers are valid for healthy myocardium ex vivo 69 CHAPTER 14 IMPLEMENTATION DETAILS what happens in for instance infarcted regions is not shown in the literature Therefore usually it is better to report volume instead of mass 14 6 Calculation of BSA The formula used is based on Mosteller wxh BSA y 4 3600 4 where w is the body weight in kg and h is height in cm 14 7 Peak ejection filling rate When calculating peak ejection and peak filling rate the volume curve is differentiated using forward difference approximation For cyclic datasets cyclic convolution is used for the calculation 14 8 Wall thickness Currently wall thickness is defined as the thickness along a radial spike from the endocardial or the epicardial center depending on set
69. bugs in Segment A summary for each of all tests that have been performed for Segment is stored in a test record file testrecord tex 17 1 Testing functionality The test functionality is implemented in the file test m It outputs the de tails of the testing result to the files testresultdoc tex testrecordtable tex and testsummarydoc tex that are used when the test report and test record are generated For an exact list of the included tests see the latest available version of the test report For each test performed a detailed list of tested functions are produced 17 2 How to write testcases in maketest m Implementing a testcase consist of two parts writing the testfunction and adding the testfunction to the list of test to perform 17 2 1 Writing test function A testfunction is written as function result testfunction result commands to test result subtest result passcriteria subtestdescription more commands to test result subtest result another pass criteria another subtestdescription In this function passcriteria is a string of tests that can be evaluated as either true or false by an eval in the function subtest The subtestdescription is a string describing the commands tested 235 CHAPTER 17 TESTING SEGMENT 17 2 2 Add test function to list of tests To add test functions to the testlist it should be grouped either into one of the already available test case if clauses in the function dotestscript
70. by looking at RV insertion points rotationslider_Callback Callback for rotation slider Update slice image pos sectorrotationhelper no Find suitable sector rotation based on RV insertion points sectors called when number of sectors is updated separatewindow_Callback Callback for separate window checkbox Updates plot setdata type datain interface function to gui to set data from code for instance reportsheet generator sliceslider_Callback Callback for slider to toggle slice startbullseye start up the bullseye analysis thissliceonly_Callback Callback for this slice only checkbox updateall Update entire GUI calls rotationslide and listbox Thats all updatelongaxisimage Update which slices are active in the longaxis image updateplot Plot different type of data Calculate retrieve data and perform graphical update This is a main workhorse updatepushbutton_Callback Callback for update pushbutton Updates plot updatesliceimage Changed the rotationslider new slice image volumeconsistent Called when volumeconsistent checkbox is called 134 15 5 REPORT SUPERUNIT 15 5 7 Pulse Wave Velocity unit The purpose of the Pulse Wave Velocity unit is to provide the user with tools for calculating and reporting pulse wave velocity data defined as the user defined distance between two planes of aortic flow images divided by the separation in time of the flow curve upslopes of these flow images
71. cardium at risk unit The purpose of the Myocardium at risk unit is to be able to do manual or automatic segmentation of the ischemic myocardium at risk of infarct from either Cardiac MR or Myocardial Perfusion SPECT MPS 161 CHAPTER 15 UNIT IMPLEMENTATION Interactions This unit interacts with the followint units Draw superunit to draw the contours and manual interactions for my ocardium at risk Calculation superunit to update volume calculations Helper functions unit to find slices with endocardial and epicardial segmentation in which the segmentation of myocardium at risk can be performed Datastructure The data is stored in the SET variable in the field MaR with the following subfields Auto Stores the automatic segmentation Result Stores the resulting segmentation from Auto and Manual Manual Stores manual segmentation or manual interactions MyocardMask Stores a mask of the myocardium i e a mask of the pixels between endocarium and epicardium MR Stores parameters specific to segmentation in CMR MPS Stores parameters specific to segmentation in SPECT Percentage Stores the resulting volume of myocardium at risk as percentage of left ventricular mass Mode set to manual if manual drawing of myicardium at risk UpdateDirectly Parameter to decide if graphical update should be performed directly Functions All functions for myocardium at risk delineation is implemented in mar m and t2wmarsegmentatio
72. chamber view 3CH Three chamber view 4CH Four chamber view 3D Three Dimensional CHAPTER 4 CONVENTIONS AND ABBREVIATIONS 3D T AA ASW ARD BPM BSA CMR CO CT DA DE MRI ED EDD EDL EDV EF ES ESD ESL ESV FWHM GUI HR LV LVM MaR MO MB MIP MPR MR MRI PET PER PDW PFR PLW PWV Time Resolved Three Dimensional Ascending Aorta Anterior Septal Wall Thickness Aortic Root Diameter Beats per minute Body Surface Area Cardiac Magnetic Resonance Cardiac Output Computed Tomography Descending Aorta Delayed Enhancement MRI End diastole End Diastolic Dimension End Diastolic Length End Diastolic Volume Ejection Fraction End systole End Systolic Dimension End Systolic Length End Systolic Volume Full Width Half Maximum Graphical User Interface Heart Rate Left Ventricle Left Ventricle Mass Myocardium at Risk Microvascular obstruction Mega Byte Maximum Intensity Projection Multiplanar Reconstruction Magnetic Resonance Magnetic Resonance Imaging Photon Emission Tomography Peak Ejection Rate Proton Density Weighted Peak Filling Rate Posterior Lateral Wall Thickness Pulse Wave Velocity 4 3 ABBREVIATIONS ROI RV RVmaj RVmin SPECT SSFP SV TOF VENC Region Of Interest Right Ventricle Right Ventricle Major Axis Right Ventricle Minor Axis Single Photon Emission Computed Tomography Steady State Free Precision Stroke volume Time of Flight Velocity Encoding limit 5 Doc
73. ck when slider is used to change slice slicethicknessedit Callback for when slice thickness is changed by user update_all Update everything on display update_line Update line upon changed line specifications update_main dummy Update main display update_preview Update preview of the reformated image 226 15 10 ANALYSIS SUPERUNIT 15 10 6 Fusion unit The purpose of the Fusion unit is to do manual fusion of two image stacks one anatomical and one functional Interactions Interactions are negligible Datastructure The image information on which to operate is taken from the SET struct and the stack number is taken from NO variable Functions anatomiccolor_Callback change colormap in the anatomical image stack map calcintensitymapping contrast brightness calculating the colormap based on the input contrast and brightness calcrotationmatrix update the functional and fusion images after flip rotation or translation close_Callback close the Fusion GUI contrast _Callback movement imagestack update the contrast and brightness in the anatomical or funcitonal image stack doflip flipparameter flip the functional image done_Callback add the Fusion image stack to the Segment main gui The Fusion image stack is built up by the functioal image and the transformed segmentation from the anatomical image drawanatomic draw the anatomical image stack 227 CHAPTER 15 UNIT IMPLEMENTATION
74. contained in the main file segmentserver m as well as the file segmentserverhelper m used for interactions 15 9 7 File menu unit The File menu unit contains functions called from the File menu Interactions This unit calls the Openfile and Database units when the user accesses them through the File menu Datastructure No use of shared datastructure occurs Functions closecurrentimagestack Callback frompreviewmenu Close current image stack i e the current image stack is deleted It also takes care of eventual cross couplings between image stacks loadednext loadnext_Callback Load next mat file in the current data folder loadsegmentation_Callback pathname filename Loads segmentation to current image stack from a seg file quit_Callback Quit Segment 201 CHAPTER 15 UNIT IMPLEMENTATION saveall_ Callback Saves all image stacks to one mat file Calls GUI method filesaveallas Callback which is the workhorse when saving image stacks fail saveallas_helper pathname filename topatientdatabase Save all image stacks to the file specified It also stores current view and modes etc savecurrent_Callback Save current image set to file Note that this is the old Segment file format and this fcn may soon be depreciated savesegdicom_Callback filename Save image stack as DICOM file savesegmentation_Callback pathname filename Saves segmentation as a seg file This way of saving contours is not recommende
75. ctor tol is numeric tolerance if omitted then set le 6 See also matlab builtin unique 115 CHAPTER 15 UNIT IMPLEMENTATION 15 4 9 mydel m MYDEL Delete file from disk OK MYDEL filename Should be platform independent See also MYCOPY RECYCLE 15 4 10 mydir m MYDIR Extracts directory information and are always first on the list AUDE cache folders cache dicomdir excluded folders comes first 15 4 11 mydisp m Internal display function 15 4 12 mydispexception m MYDISPEXCEPTION ME Pretty prints a caught exception for debugging ME is matlab error struct caught in a try catch clause See documentation on try and catch syntax 15 4 13 myecgreader m 15 4 14 myexecutableext m MYEXECUTABLEEXT Returns proper file extension for exectutables See also MYREQUIREPC MYMKDIR MYMOVEFILE MYCOPYFILE MYDEL MYDIR 116 15 4 HELPER FUNCTIONS SUPERUNIT 15 4 15 myfailed m MYFAILED STRI FIGHANDLE Displays an error message STRI FIGHANDLE is an optional alignment indicating alignment Difference to errordlg is the alignment and possibility to hit return to okey the message Alignment string may be a fig handle or an MYGUI object See also MYWARNING MYMSGBOX MYADJUST MYWAITBARSTART 15 4 16 mygetcurrentpoint m Returns CurrentPoint of an axes h In case of macro or testing returns current point from buffer 15 4 17 mygetedit m Get string from an edit box Use this instead of get h St
76. culation Currently 3D visualization does not take this flag into account This will be addressed in future versions Position of the rotation center in the image stack y coordinate Left ventricle stroke volume Identified scanner identified by parsing the DI COM tag Manufacturer Presented values are e ADAC e Bruker e GE e Philips e Siemens e Suinsa e Toshiba This is a struct containing information for viabil ity analysis For details about the algorithms and internal representation please see 15 6 6 Rotation of the Sector compartmentization of the left ventricle used for regional myocardial analysis Unit is degrees This is can be manually adjusted from the bulls eye GUI Name of the sequence taken from DICOM tags 63 CHAPTER 13 SET VARIABLE SeriesDescription Series description of the image serie taken from SeriesNumber SliceGap SliceThickness SpectSpecialTag StartAnalysis StartSlice Strain StrainTagging Stress 64 DICOM tags Series Number taken from DICOM tags Gap between slices in millimeters if present Read from DICOM file by looking at the tag SpacingBetweenSlices if present If not present then the DICOM tags ImageOrientation and ImagePosition plus SliceThickness from above are used Thickness of slices in millimeters Read from DI COM file by looking at the tag SliceThickness If not present then the tags ImageODrientation and ImagePosition are use
77. d Read from DICOM file for determination of the image tag ImageType in SPECT images Valid inputs are Rest Rest Prone Stress or Stress Prone Time frame for start of analysis used in flow quan tification See Reference Manual for details De fault value is 1 This field contains the first slice in the set of se lected slices For more details see below This is a struct containing information for strain analysis from velocity encoded MR images For details about the algorithm and internal represen tation please see 15 10 3 This is a struct containing information for strain analysis from tagged MR images Reserved for future usage StudyID StudyUID TDelay TIncr TimeVector TSize VENC View XMin StudyID taken from DICOM tags StudyUID taken from DICOM tags Trigger delay i e starting of image acquisition af ter trig pulse Read from DICOM tags if pre sented otherwise set to zero Given in seconds Currently unused Time increment in seconds between time frames Must be non zero when image stack is time re solved If increment between time frames is not uniform the value contained here is the mean time increment Vector containing time position of each timeframe Size of image stack in temporal direction The following two expressions are equivalent SET NO TSize and size SET NO IM 3 Velocity encoding range in MRI pulse sequence Read from DICOM tags if presente
78. d and may be depreceiated savetopacs_Callback Send image stacks to PACS This function should display a list of available PACS con files and when user has selected store files on disk temporarily and then send the files to the PACS savetopatientdatabase_Callback Callback to save image stacks to patientdatabase Uses functions in patientdatabase 15 9 8 Utility unit The utility unit contains tools that operates of files mat files or DICOM files rather than the loaded image data Interactions The Calculation superunit is called to calculate image data The Open File unit is called to open files Datastructure The utility uses and also generally resets the SET structure so that unsaved image data is lost 202 15 9 FILE SUPERUNIT Functions This function recommends that you set RV insertion points in or der to have the bullseye correctly rotated If no insertion points are marked then cur rent rotation are taken ahaexporthelper type Helper function to export in 17 segment model clearsegmentationmultiple_Callback This function clears the segmentation in multiple mat files This is useful for instance in research and when second observer analysis is required findindicomfiles_Callback recursevily finds mat files in selected directory and exports data on patient info and file location Uses some heuristic to avoid checking all files findinmatfiles_Callback recursevily finds mat files in selected
79. d otherwise set to zero Given in centimeters per second Struct that stores information of the current view Used to retain the same view after saving an image stack Only SET 1 View is filled When loading images it is possible to crop the im ages XMin contains the number of pixels that the contours are translated due to cropping compared to the original image size When no cropping is performed XMin is 1 65 CHAPTER 13 SET VARIABLE XSize Size of image stack in X direction The following two expressions are equivalent SET NO XSize and size SET NO IM 1 YMin Same as XMin except relates to the Y direction YSize Size of image stack in Y direction The following two expressions are equivalent SET NO YSize and size SET NO IM 2 ZSize Size of image stack in Z direction number of slices The following two expressions are equiv alent SET NO ZSize and size SET NO IM 4 66 14 Implementation Details This chapter contains the implementation details given in the Segment User Manual 14 1 Version handling A proper version handling is employed when developing Segment A detailed version history of Segment is found in the revision log of Segment SVN 14 2 Numeric representations All numbers are stored and used internally as double precision floating points with the following exceptions e Images are stored as single floats normalized or as integers uint8 and then as they are stored in the DICOM
80. d separated with a NaN so that drawing of the endocardial con tours can be done with a single command The correspondence for the Y coordinates to EndoXView Same as above but for the epicardial contour Epicardial interpolation points Epicardial interpolation points Corresponding to EndoPinX Corresponding to EndoPinXView Corresponding to EndoPinY Corresponding to EndoPinYView Epicardial contour otherwise same as EndoX EpixView EpiY EpiYView FileName FlipAngle Corresponding to EndoXView See above Corresponding to EpiXView Filename of the file storing this image stack Flip Angle in MRI pulse sequence Read from DI COM tags if presented otherwise set to zero Given in degrees 49 CHAPTER 13 SET VARIABLE Flow 50 This struct contains information regarding how different image stacks are related to store flow information Generally all information that are common for all the coupled image stacks are only stored in the magnitude image stack to avoid data redundancy One example of this is storage of ROIs that are only performed in the magnitude image stack The Flow struct contains the follow ing fields e Angio contains a reference to which image stack that contains the angio imag This an gio image is essentially the absolute value of the velocity times the image magnitude and could be useful for vessel identification Nor mally this field is set to an empty vector as the angio
81. d to flip both z and x to maintain a righthand system flipz_helper Helper function to flip in z direction Takes care of segmentation flipzt_Callback Interchange z and t for current image stack Takes care of segmentation imageinfo_Callback arg Displays image information of current image stack intensitymapping_Callback Plots intensity mapping function invertcolors_Callback Invert colors in current image stack essentially 1 x Need to fix more to get intensity offset correct kspace_Callback Shows KSPACE of image Fourier Transform Displays the log of the Fouries Transform mirrorx_Callback Mirros in x direction Need to flip both x and z to maintain a righthand system 174 15 8 TOOLS SUPERUNIT normalize_Callback Normalize image data of current image stack Make sure image intensities are in the range 0 1 Also stores in so that true image itensities can be retrieved see calctruedata opensetimagedescription_Callback Open the gui for setting the image type image view plane and imaging technique for current image stack precomp_Callback Function to make intensity precompensation of MR gradient echo images This function is somewhat obsoleted removeallbutedes_Callback Remove all timeframes in current image stack except diastole and systole removeallbutthistimeframe_ Callback Remove all timeframes except current timeframe removecurrenttimeframe_Callback Remove current timeframe removedupl
82. ddenchars m On the second level there are the studydate a dash the characters ID a dash and the for last dig its of the studyuid i e 20061204 ID 7232 On the next level there are folders with series and in each folder there are DICOM files In this folder there is also stored a file called thumbs cache this file con tains thumbnail previews of all the series For more details see the file thumbnails m for details If changes are made to the design of this filestructure corresponding changes should also be made in the Segment DICOM server e Report this folder stores the html reports created by the Report Sheet unit Please see the Report Sheet unit for further details e TEMP this folder is used to temporarily retrieve images in the PACS connection When images have been retrieved they are automatically 197 CHAPTER 15 UNIT IMPLEMENTATION moved to the patient database It should not be necessary to manually remove files from this folder e TEMPSTORAGE this folder is used by the Segment Server to temporarily store received files After sorting they are automatically stored in the patientdatabase It should not be necessary to manually remove files from this folder Datastructure The patient database function contains a global variable called DB Handles stores the handles of the GUI NumStudies contains the number of studies CurrentStudy points to the current study SortList is a vector and contains the current so
83. de BOG RR DOR Bie 120 ee ee a 120 pios lee wee Bw br 120 ee eee A eh ese ee ase e 121 o Gee Shaye oe eee Aes E 121 etek Boe eee Ape Geo ee gene eae o 121 aes oe Ae oe Ge eae eis a ee E 121 CONTENTS 15 4 34 myuigetdir m 0 4 30 myuigetfile m a Ae A ee A A 15 4 37 myurlread m ns ies ads o EEEE o sa A re ee a a kee as ira ok ees re ree re ate oe hoe eae ee oe eee sp ook oo ye ee ee eee eT ere eee rr eres 15 4 4 myworkon m A 15 5 Report superunit coso cria 864s ek oe we RO 15 5 1 Report 3D unit 15 5 2 Report Volume unit 15 5 3 Report Radial Velocity unit 15 5 4 Flow unit crasas A 15 5 5 Report Slice unit 2 lt 44 lt lt 6 44 444 es sn 15 5 6 Report Bullseye unit 15 5 7 Pulse Wave Velocity unit 15 5 8 Qp Qs Valve unit ca ee as a 15 5 9 Unwrap unit 15 5 10 Report Sheet unit a 4 es a ee a 15 5 11 Export unit 15 6 Segmentation superunit 15 6 1 Measurement unit 2 204 15 6 2 Annotation point unit 15 6 3 LV segmentation unit 15 6 4 KV segmentation unit lt lt o lt oocoooc s 15 6 5 Contours unit 15 6 6 Viability unit 15 6 7 Myocardium at risk unit 15 6 8 ROI analysis unit lt lt lt 15 7 Resources superunit 15 7 1 Help unit 15 7 2 Preferences unit vi CONTENTS
84. ders playcurrentslice Plays the current slice refocus Gives back focus to slider4 which has keypressedfcn set to the callback handling all keyboard shortcuts Of course we would like to give focus to the figure itself and let the figure handle the keypresses but matlab won t let us do that Yes this is a hack to get around a matlab limitation slider4 is placed at 100 100 so it shouldn t cause any trouble sliceslider_Callback Slice slider callback timeframeslider_Callback Timeframe slider callback unwrapcurrentpixel updown Unwrap current pixel in specified direction 139 CHAPTER 15 UNIT IMPLEMENTATION unwrapped unwraptimeseries wrapped jumpsize varargin function unwrapped unwraptimeseries wrapped jumpsize jumpfraction debug Unwraps a timeseries of samples unwrapped The unwrapped phase wrapped The wrapped phase jumpsize Size of the expected jumps in the data jumpfraction Fraction of jumpsize to consider a jump Default is 0 5 debug Perform sanity checks on input Default is true but can be set to false for speed Example usage when SET NO is a phase stack SET NO IM x y slice unwraptimeseries SET NO IM x y slice 1 0 5 updatecurrentpointoverlay Updates the current point overlay red square in velocity image updatefullgui Updates all gui elements to reflect current state updatepanimagesliders Updates the pan image sliders invisible if zoomlevel is
85. down function for timebar axes of image specified by input parameter field Changes current timeframe to the one closest to position of clicked point 213 CHAPTER 15 UNIT IMPLEMENTATION timebaraxes_ButtonUpFcn hObject Buttonup function for timebar axes of image specified by input parameter field Deactivates dragging of timebar timebaraxes_MotionFcn hObject tbobj no field Mouse motion function for timebar axes of image specified by input parameter field Used for dragging timebars to change current timeframe or start end points of timeframes in which to align images setstr timestripset setstr tsz t0 t1 From a SET struct that has been stripped of some timeframes removes information specific to discarded timeframes updateplot field Update plot of upslopes from image specified by field argument updaterotatehandle midpoint ang h Update rotation handle specified by handle h from input arguments updatetimebar h no Update timebar axis specified by handle h from input arguments 15 10 3 Strain unit The Strain unit allows to calculate strain from velocity encoded phase con trast images Interactions The function interacts with the Helper function unit and the Calc unit Datastructure The module uses an own data structure in the field SET Strain Functions timestepapex timestepapicalr timestepapicall timestepmidr timestep midl timestepbasr timestepbasl ca
86. e Detection in Multidimensional Im ages PhD thesis 91 85297 10 0 Linkoping universitet Department of Biomedical Engineering 2004 E Heiberg L Wigstrom M Carlsson A F Bolger and M Karlsson Time Resolved Three dimensional Automated Segmentation of the Left Ventricle In JEEE Computers in Cardiology 2005 volume 32 pages 599 602 Lyon France 2005 H Engblom M B Carlsson E Hedstrom E Heiberg M Ugander G S Wagner and H Arheden The endocardial extent of reperfused first time myocardial infarction is more predictive of pathologic Q waves than is infarct transmurality a magnetic resonance imaging study Clin Physiol Funct Imaging 27 2 101 8 2007 N R Ghugre C M Enriquez T D Coates Jr Nelson M D and J C Wood Improved R2 measurements in myocardial iron overload J Magn Reson Imaging 23 1 9 16 2006 G Granlund and H Knutsson Signal processing for computer vision Kluwer Academic Publishers Linkoping 1995 ISBN 0 7923 9530 1 O Adeyanju E Heiberg and J Sjogren Automated calculation of T2 mapping for MR images with application of certainty criterion for en hanced display In ISMRM 18th Scientific Sessions Stockholm 2010 247 BIBLIOGRAPHY 8 10 11 12 13 248 J Tufvesson E Hedstrom K Steding Ehrenborg M Carlsson H Arheden and E Heiberg Validation and development of a new automatic algorithm for time resolved segmentation of the left vent
87. e always dividable by three The slices are divided into equal thirds for basal mid and apical parts Interactions Interaction with the calculation unit to perform underlying calculations The Export unit is called for export of data Datastructure The data in the unit is stored as a mygui object with the following fields e volumeconsistent boolean and true if volume consistent checkbox is enabled e numsectors number of sectors in the bullseye plot 131 CHAPTER 15 UNIT IMPLEMENTATION e slice for which the image with spoke wheel is plotted e outdata variable extracted with data from SET depending on user selection e ahaoutdata variable with extracted data in aha 17 segment format Fun stri Ge ctions ypos ahal7nameandpos i t name of 17 segment im bullseye m ax n vc no tf Calculate bullseye from matrix m Ax is optional axis where the output image im should be displayed m ax n vc values in the sectors figure axes number of pixels in the resulting image volume consistent true or false im resulting bullseye image varargout bullseye2 m ax n flipx vc no Generate bullesye data Optional output argument is im m values in the sectors ax figure axes n number of pixels in the resulting image fl vc ipx flip in x direction true or false volume consistent true or false varargout bullseyeaha m ax n valuetype Calculate and or plot A
88. e file reader unit This is the reader of mat files and DICOM files The file segloader m defines a class used for loading files into Segment the file segdicomtags m defines a class for handling DICOM tags and the file segrawstack m de fines a class used for rendering Segmentimage stacks from DICOM data This class also has a subclass defined in rotrawstack m for loading image stacks where the image plane has been rotated between capture of slices For loading DICOM images a segloader m object is created which in turn creates a segdicomtags m object for keeping track of DICOM tags and a segrawstack m or rotrawstack m object for rendering an image stack Interactions Interactions are negligible Datastructure No use of shared datastructures occurs 183 CHAPTER 15 UNIT IMPLEMENTATION Functions in segloader m adddicomfiles self filenames Adds DICOM files to the object addmatfile self filename Adds a mat file to the object r getpreviewdata s fname Gets an element from a struct if it exist and has type char else return Used for generating preview h hour tfrac Convert from tfrac to hours r imaxis isrotated self Checks if the loaded files is a rotated image stack eq linecmp linel line2 Used to compare two lines generated by uniquelines Accepting some errors m minute tfrac Convert from tfrac to minutes curdicoms removeduplicates curdicoms Removes any duplicate
89. e images of the endocardium have been calculated True if the edge images of the epicardium have been calculated Temporary variable used to store one frame of a movie when recording a movie using the movie recorder in Segment Number of points along the endocardium epi cardium and ROIs This default set to 80 This variable should be possible to change to get more points along a contour but this have not been veri fied or tested Note that changing this variable will most probably cause version incompabilities with seg and mat files 41 CHAPTER 12 DATA OBJECT BpInt MInt Pin Measure Cursor NeedToSave Testing RecordMacro Macro MacroN Buffer CineTimer contourp contourbimage 42 Intensity in the blood pool of the image stack SET NO This is used to avoid unnecessary recal culations of DATA BALLOON Intensity of the myocardium of the current image stack See above Keeps track of pins Contains measurement data such as offset and co ordinates of points Contains cursor data such as location and offsets True if there are changes that need to be saved Used by maketest to tell a program when it is being tested Used by macro_helper to tell when a macro is be ing recorded Used by macro_helper to keep track of the macros in a list Used by macro helper to keep track of the posi tion in the Macro list Contains pending actions used for macros and test ing
90. e stack mu my2means vec Special case of k means when k 2 v nanremove v Replace NaN with zeros final remove_holes a The function removes hole in an ND image viabilityapexpostprocessing Callback Toggle setting viabilityautoem Automatic viability using the method in the EM algorithm viabilityautofwhm Automatic viability using the method in the Radiology paper viabilityautootsu Automatic viability using the method in the Outsu method viabilityautosdfromremote Automatic viability using the method SD from remote 159 CHAPTER 15 UNIT IMPLEMENTATION viabilityautoweighted Automatic viability using the method in the Radiology paper viabilitycalc force Automatically calculate viability This is the workhorse Different options for calculation se as Scar Mode If force is not true then ask if stdlimit 1 8 viabilitycalcbutton_Callback Callback to recalculate the viability viabilitycalcvolume no intweight Calculates the volume of the viability viabilityclear_Callback Callback to clear scar data viabilityclearmanual_Callback Callback to clear manual interactions viabilityclearmanualslice_Callback Callback to clear manual interaction in current slice viabilityclearslice_Callback Callback to clear viability for current slice viabilitycreatemask no Helper function to create the myocardial mask viabilitygetsd_Callback calculate nbr of sd based on auto manual scar segmen
91. ect 33 45 67 14 1 Version handling css a e e a ah 67 a e a BOR Sue a 67 ESE aie 67 14 4 Volume calculations oscar ea e a 69 14 5 Mass calculations 2 6 2024 bs e od 69 e o ee beet e eb 70 ee le E E E E E EEE 70 14 8 Wall thickness 2 0 0 0 0 000000000 000004 70 Eade ssp poss 71 14 10 Infarct size extent and transmurality 71 14 11 Number of SD from remote for Scar 72 aro paa 72 A NN 73 14 122 Smoothing c e ws bok oe a a te a eS 73 a A A Ee A es Os 74 CONTENTS 75 15 1 Main Segment superumit o 2424 75 15 2 Draw superunit 224 2 recrear A 100 15 3 Calculation superunit ov 3 ee2e3d6 aia ld de 105 15 4 Helper functions superunit 110 1541 Find nit se bo See a we oe DR Awe ee i 110 DAS Exist UDU cc oe 8 be eee Be Ob oe ead eS 112 15 4 3 Input Output unit ae ook ee De ew es 113 ink a Rt IE 114 Bg te dei Sahay ecg BH iat Ge ee a Se S 114 TE 114 a e ps A a Ds 115 Ps ee ee 115 aa ee eee ee das en oe ee 116 EAN A 116 NN 116 e e a ee re E 116 A eh as ee tee he eee te 116 oe e eee 116 oon ee ew GA era ee A ee 117 a ee ias le ai eee 117 RE da E Sis Se ee ee a E 117 E E oe ee oe ee oe 117 Grist eR Gye eee He ee ee a 117 Sa pea Ra pe A a a 117 eee E E 118 OW de BAe Ale o A ne ak eet por 118 bt th Oe Pe Bae Bos ek be ee bee 118 oe CASE RAP AA e dE Bs 119 be A sds i ds ee Ge os we Ba we PSS 119 ee eee EEE ee eee 120 Phd oh A
92. ectra Starts the SECTRATIMER The timer executes function loadsectra every second loadsectra Load files from sectra pacs varargout sectra varargin Switchyard for sectra module stopsectra Stops the SECTRATIMER if it s running Files on plugin side e maind11 This is a main template file from the SDK e sectracontrol This file is related to the interface such as status texts etc e pipe This is the main file written by Jonatan First it finds Segment and then starts Segment unless it is already started The file contains of the following sections 205 CHAPTER 15 UNIT IMPLEMENTATION 1 write_info writes the control file info file 2 write_dicom called by server_thread 3 server_thread this file can be seen as the main function that created the pipes by calling the subfunction create named pipe The function Connect_Named_Pipe takes time and waits for some one to read e write_dicom Writes the DICOM files The term dicomattrib is the Sectra name standard and corresponds approximately to dicomtags The Sectra term Pyramid corresponds approximately to one DICOM file The preview file is as mentioned above legacy and is not used Each time a file is sent them check for errors are performed The function SendVR uses get_VR by Sectra API The function SendData sends data depending on VR and peforms changes in the data representation 15 9 10 External PACS unit The External PACS unit consists of a Segment side imp
93. ence Manual Functions e segpref m contains all callbacks and GUI code for the main and ad vanced preferences GUI s e pacspref m contains all callbacks and GUI code for the PACS prefer ences GUI e loadpreferences loads the preferences file and stores the information in the data structure This function contains an important subfunction called preferencesbackward that handles backward compability for older Segment versions 15 8 Tools superunit The purpose of the image tool unit is to provide tools to perform on image stacks 170 15 8 TOOLS SUPERUNIT Interactions This unit uses the Calculation superunit to make calculations for some ad vanced tools and the Helper functions superunits to check for existence of image content to be copied to other stacks Datastructure No specific datastructure is used for the tools Functions addnoise_Callback f Adds noise to current image stack anonymous_Callback silent newname Makes a data set anonymous by removing PatientInfo PatientInfo PatientInfo FileName OrigFileName PathName Name ID BirthDate anonymoustotal_Callback silent newname Makes a data set completely anonymous by removing PatientInfo PatientInfo PatientInfo PatientInfo PatientInfo PatientInfo PatientInfo PatientInfo PatientInfo PatientInfo FileName OrigFileName PathName Name ID BirthDate Sex Age AcquisitionDate Length Weight BSA Ins
94. ences in the database needs to be recomputed This can be done by rebuilding the database available from the menu This also helps if the database for some reason have become corrupted Functions The function is called patientdatabase m and also calls the function patientdatabaseaddstudyhelper m 15 95 PACS unit The purpose of the PACS unit is to enable Segment to connect to a hospital PACS system and retrieve images The functionality of the PACS connec tion unit is documented in detail in the Patient Database Manual and PACS Communication Manual All low level communication is performed by the DCMTK toolkit for docu mentation see http support demtk org docs index html Searches can be performed both on patient level and study level Interactions All interactions with Segment is performed through the patient database 199 CHAPTER 15 UNIT IMPLEMENTATION e The connections are stored as structs in mat files and is stored in the Segment main folder e Logfiles are stored in the same folder as where the preferences are stored e It is also possible to store batch files for downloading They are also stored as mat files e Temporarily files in the download process are stored into the folder TEMP located in the same place as where the Patient Database is stored this is configured in the preferences menu Datastructure The internal data used by the GUI is stored in the mygui struct Functions The
95. ent updateicons JU out viabilityallowweighted Return whether to allow weighted viability mode 99 CHAPTER 15 UNIT IMPLEMENTATION 15 2 Draw superunit The purpose of the draw unit is to perform all graphical update of image panels in Segment Interactions This unit calls the Calculation superunits to help calculate some of the details that are to be drawn Datastructure The functions uses the SET structure and the fields rows and cols are especially important since they contain the number of panels Other important data structure are in the DATA object 1 ViewIM contains a cell array of preprocessed images ready to be dis played One for each available image panel The images are either RGB images or uint8 images that goes to grayscale mapping 2 ViewMatrix contains the number of image panels available on the screen in the current view mode 3 ViewPanels a vector that linkes to the image stack number for each panel For non active panels the number is zero 4 ViewPanelsType a cell array with the type of each image panel Functions s cellref a varargin Returns vector of content of e varargin for all elements e of cell a drawall n m Draws all panels that should be visible or up to the number specified as n If called with n then lookup from imagepanels When n m specified draw n m panels drawallslices This fcn updates graphics in all visible image panels 100 15 2 DRAW SUPERU
96. ent Handle to the main GUI figure A list of open figures that contains GUI s that are sensitive to changing the current image stack NO Handle to the figure where the images are plotted Currently this is same as fig but are reserved for future use True if image data is present True if no graphical output should occur This is usefull when writing plugins that perform batch processes Struct with all graphical handles in the main GUI When set to true new calculation initiated from callbacks are prohibited This may be obsoleted in the future and replaced with Matlab s queueing properties 33 CHAPTER 12 DATA OBJECT Undo UndoN LastSaved Volrend ViewPanels ViewPanelsType ViewPanelsMatrix 34 Struct containing undo information Scalar that contains a pointer in the undo history list Time stamp when the image stack s last were saved This is used for the auto save functional ity Reserved for future use with the future volume ren dering module A vector pointing to image stacks If 2 x 2 pan els are shown on the screen then the length of ViewPanels is 4 For panels that does not contain any image stack the corresponding pointer is set to zero A cell array where each element contains the view mode for each image panel Allowed view modes are e mode one shows the image stack as one slice e mode montage shows all slices of the image stack arranged in a matrix style e
97. entery 215 CHAPTER 15 UNIT IMPLEMENTATION centerx centery inside centerline x y Calculates center line and returns wich points x y is contour clearall_Callback Clear all strain data for current image stack clearandcalculate_Callback Callback to re initialize mesh closestrain_Callback close the strain gui index contourindex2node no x y Find connection between points on contour and boundary points index is length contour correctionpoint_Buttonup This is called on mouse up correctionpoint_Motion This function is called when user moves the point correctionpointbuttonuphelper x y Helper function to correctionpoint _Buttonup and anatomicalcorrectionpoint _Buttonup x y are assumd to be in strain coordinates correctionpoints_Buttondown Called when someone clicks on a point on strain image correctionpointsbuttondownhelper x y motionfcn upfcn Helper function for buttondown for correction points ok errorchecking no Error check before calculate strain Checks for existance of segmentation and if not try to import segmentation from cine images exportlongaxis_Callback export strain data from one long axis projection to clipboard 216 15 10 ANALYSIS SUPERUNIT exportstrain_Callback Read in strain from files in a folder and export them to clipboard exporttocine_Callback Written by Einar Heiberg Export strain segmentation to SSFP image apex findapex x y pmin pmax Find a
98. er draging center point center_Motion Motion function of the center point centeronslice slice no zsz Put slice in center of montagefit view changewheel_Callback h e scrollwheel with modifer Tab are not included but you can if you like checkconsistency timeframes slice Check consistency to prevent earlier manual segmentations that have problems with direction lef right 76 15 1 MAIN SEGMENT SUPERUNIT xout yout checkconsistencyhelper xin yin Make sure that the contour is counter clock wise and that it starts at three o clock Also ensures that the points are evenly distributed corrupted checkcorrupteddataforautomaticsave setstruct This function checks if the data SET is corrupted due to corrupted loading when loading files which has been saved with older saveversion see ticket 502 in wush for more details on the bug cinetool_Callback Starts the cinetool that allows simultanues segmentation at the same time as it plays clickedpin_Callback type Called when user clicks on a pin contrast _Callback arg panel Activated by contrast tool different from resetlight Callback above mask createmask outsize y x Function to generate a mask from a polygon represented with the vectors x and y ctrle function to handle ctrl c keypress which is disabled do doatrialscar no Helper function to check if user input is for atrial scar or lv scar default doputpin Callback type Put pins Cal
99. ers that needs to be passed to the functions The drawback with using global variable is that the variable should at all times only reflect valid global states of the data Therefore it is very impor tant that modifications of the global variables are done with care 29 11 Class Hierarchy Overview This chapter documents the class hierarchy of Segment The implementation of Segment is only partially performed using object oriented techniques and the main reason for this is that object oriented Matlab was not possible to compile at the time when the oldest part of the code was written 11 1 General class hierarchy The general class hierarchy that partially constitutes Segment consists of a main GUI superclass maingui and its software specific subclass such as the cardiac research edition Segment subclass segmentgui the cardiac MR clinical edition Segment CMR subclass segmentmrgui and the cardiac CT clinical edition Segment CT subclass segmentctgui An overview of this hierarchy is provided in Figure Main GUI superclass Segment CMR GUI subclass clinical MR edition Segment CT GUI subclass clinical CT edition Segment GUI subclass research edition Other GUI subclasses not documented here Figure 2 Overview of the general GUI class hierarchy 11 2 Compilation class hierarchy The class hierarchy for compilation consists of a superclass makeitclass and its subclasses For compilations of Segme
100. es Pixelspacing in X direction in mm vertical direction in Segment This is taken from the DICOM tag PixelSpacing Pixelspacing in X direction in mm horisontal direction in Segment This is taken from the DICOM tag PixelSpacing Velocity encoding VENC in cm s For non velocity encoded images 14 4 VOLUME CALCULATIONS this should be 0 How this is interpretated involvs proprietry informa tion of different scanner vender information e Rotated image stack This should by default be false If your image stack is rotated then change this to true Currently this parameter is not taken from information in the DICOM tags and the user needs to manually change this when loading rotated image stacks e Cyclic image If the image stack is cyclic i e covers the whole heart cycle this should be true default For prospectively gated image series this should be false This affects mainly the automated segmentatin algorithm Currently this information is not read from the DICOM information 14 4 Volume calculations The volume calculations are done by a summing the area in each slice The main reason for not using a more advanced volume integration method is that no one else is using that and therefore it might be difficult to compare the results Segmentation i e delineation of endocardium and epicardium is stored on a sub pixel accuracy and subsequent calculations are on a sub pixel basis For viability the classification into via
101. es but systole and disastole 95 CHAPTER 15 UNIT IMPLEMENTATION segmentclearalllv_Callback g force Clear all LV segmentation both endo and epi Overloaded in CVQgui segmentclearalllvbutsystolediastole_Callback g Clears all LV segmentation except in systole and diastole Overloaded in CVQgui segmentclearallrv_Callback g force Clear all RV segmentation both endo and epi Overloaded in CVQgui segmentclearallrvbutsystolediastole_Callback g Clears all RV segmentation except in systole and diastole Overloaded in CVQgui setprefhandles g Called by segpref main Overloaded in CVQgui since uses another fig setthisframeonly g value Callback to set this frame only mode startlog log Start Segment log stoplog Stop Segment logging switchtoimagestack g no force This function makes no current image stack and updates graphics switchtoimagestack_part2 g no switchtoimagestack continued Overloaded in SegmentGUI and CVQgui thisframeonly_Callback g thisframeonly silent Sets segment in this frame only mode Changes made to segmentation copying etc are performed only for the current timeframe togglescar g Called by segment updateviewicons Overloaded in CVQgui 96 15 1 MAIN SEGMENT SUPERUNIT updateaxestables g arg varargin Method to update AxesTables in GUIs where present updateedes Overloaded in CVQgui updateicons g mode Updates icons when new mode is selected Ove
102. es mesh x and y are the curve of the myocardium Uses initmesh in PDE toolbox keypressed fignum evnt Keypress callback laplaceradiobutton_Callback User clicked laplace radiobutton multiplebullseye_Callback Plut multiple bullseyes from clipboard navierradiobutton_Callback User clicked Navier radiobutton nedit_Callback Edit number of points n nslider_Callback User changes the nslider nyedit_Callback User made changes in edit box 218 15 10 ANALYSIS SUPERUNIT nyslider_Callback User drags the nyslider u c optimizingcoeff no vx vy A c K H Optimze the coefficients run an optimization scheme vx is velocity field vy is velocity field c is coefficent matrix plothelper type Helper function to plot parameter Uses the information in the handles parameterlistbox plotmax_Callback plot the strain value from the time frame with abs maximum strain over time plotmin_Callback plot the strain value from the time frame with abs maximum strain over time polarplotaha strainvalues ax plot the aha model in the polar plot dist projection p plane Calculates distance d to plane given by p1 p2 Calculate nhat normal of plane propagatendoseg no Propagate node points recursekeypressfcn h fcn Helper function to create callbacks to keypressed function resetstrain no Clear strain data with new format for the internal representation retrack no Recalculates the mesh takin
103. example mywarning mymsgbox and yesno when calling with last input argument as the mygui object Example First reserve space for it in DATA Structure DATA GUI MyGUIExample in segment m In your code to initialize gui mygui myguiexample fig In your subfunctions global DATA 118 15 4 HELPER FUNCTIONS SUPERUNIT gui DATA GUI MyGuiExample Now you can use gui as an ordinary variable and everthing is stored in the GUI and will be available to other subfunctions until the GUI is deleted Some examples gui myfieldname somearray gui myfieldname1 myfieldname2 myfieldname3 134 temp gui myfieldname 2 temp get gui handles text2 string You can also use the gui to get good alignment of the msgboxes mywarning myfaield mymsgbox mymenu mywaitbarstart and yesno myfailed An error has occured gui When closing the gui the close function can be called with DATA GUI MyGUIExample close DATA GUI MyGUIExampl1e when closing by using this syntax the position of the gui will be saved in the struct DATA GUIPositions The position of the gui can also by saved by saveguiposition gui this could be used in a resize function See also SUBSREF SUBSASGN 15 4 24 myguide m MYGUIDE Same as GUIDE but can also open fig files located in package directories without having to change directory manually 15 4 25 mymaximize m MYMAXIMIZE HANDLE Maximizes a figure or a mygui ob
104. f if a gt bl d lt e MLINT syntax guidelines should be followed and ideally when syntax hints are overrided they should be motivated For instance when MLINT reports Warning data seems to grow inside a loop and that you should consider to preallocate for speed Then before inserting a pragma to remove the warning you should make a note on why you did not preallocate which usually is that the routine is not time critical but is should generally be documented Another example is when MLINT warns that the variable is unassigned but it is assigned by loading a mat file then this should be commented The use of logical short cutting operands and amp amp is strongly recom mended 6 10 Documenting code The source code should be well documented so that new programmers easily can understand the code Note especially that the part of the code that was trickiest to write also deserves the most comments Functions should be written as Explanatory help text of the function Help text may span multiple lines 16 6 10 DOCUMENTING CODE Your code begins here It is very important to follow this coding standard since part of this doc umentation is automatically generated from the source code 17 7 Coordinate Systems This chapter specifies the coordinate systems used in Segment 7 1 Introduction DICOM specifies coordinates in the RL right left AP Anterior Posterior and FH Feet Head coordinate system Internal
105. files Most functions in Segment will automatically convert the data to floats e Edge detection results are stored as integers 16 bits normalized e Character strings are stored in 8bit ASCII format e Infarct maps are stored as int8 manual interaction and uint8 result e General segmentation tool store objects as levelset function with an uint8 representation where the zero levelset resides at 128 Internally the image stack is normalized upon loading by a global maximum intensity such that all values are 0 1 Offset and scaling is also calculated so that the image stack can be reconverted back to original signal intensities 14 3 Loading data and interpretation of DICOM tags This section describes how Segment interprets DICOM information to cal culate important parameters suchs as geometric properties of the images e Number of slices This is calculated from the presence of different slices based on the DICOM tags ImagePosition and ImageOrientation 67 CHAPTER 14 IMPLEMENTATION DETAILS 68 Number of timeframes This is based on dividing the total number of images with the number of slices Time increment in ms between each timeframe If uniform this is based on the difference between the number of timeframes divided by largest and the smallest value of the DICOM tag TriggerTime If the DICOM tag TriggerTime is not present then the DICOM tag TR is used as time increment Note that this might depent on your k sp
106. for ex ample added into the loaddicomfiles caluse or a new test case clause should be added In the test case if clause the test function is added to the testlist by the following commands testlist addtest testlist shortdescirption longertestdescritption boolean testfunction Where short description and longer description describes the purpose of the testfunction the boolena is either true or false true if all image stacks should be closed before starting test oterwise false and testfunction is the name of the function to test If a new test case is added it will have to be added in the function testcaseselector as well so that it is possible to select the test case when running maketest 17 3 Testing broken callbacks Testing broken callbacks is tested by the function validatecallbacks Called with one input argument it tests the fig file in the input argument and prints result in the standard output If called with no input arguments then the entire Segment project is tested and a report is written to the file callbacksdoc tex which is used to produce the test report The test script assumes that the first argument in a callback string is a sub function in the function name in the callback string if applicable The script tests uimenu uicontextmenu and uicontrol objects that has a callback string defined To parse out sub functions of a function the function document m is used 236 18 Compiling Segment 18 1 In
107. frame ind findslicewithendoall no Find slices with endocard in all timeframes ind findslicewithepi no Find slices with endocard in any timeframe ind findslicewithepiall no Find slices with endocard in all timeframes ind findslicewithmarall no Find and return slices with mar 111 CHAPTER 15 UNIT IMPLEMENTATION ind findslicewithrvendo no Find slices with RV endocard in any timeframe ind findslicewithrvepi no Find slices with RV epicard in any timeframe ind findslicewithscarall no Find and return slices with scar 15 4 2 Exist unit The purpose of the Exist unit is to contain functions that assist other func tions in determining whether some segmentation content exists in a given slice or stack Interactions Calls to other superunits are negligible This unit is commonly used in the test script in order to check if operations have been successful Datastructure The Exist unit tools search the SET struct for existence of requested infor mation Functions z anyall a Equivalent to z any a y existendo no True if endocardium exist in some slices y existendoinselected no t s True if endocardium exists in selected slices If argument is specified only look in timeframe t y existendoinslices no t True for the slices where endocardium exists If argument is specified only look in timeframe t oterwise look if there is endocardium in any time frame 112
108. g This function would benefit from anti cut and paste treatment removeallinterp_Callback silent no arg indarg Remove all interp points removeallpins_Callback silent endo epi rvendo rvepi Remove all pins removeallpinsthisslice_Callback current endo epi rvendo rvepi Remove all pins in this slice removepin_Callback type m Removes pins removethispins_Callback endo epi rvendo rvepi Remove pins in this slice and timeframe resetedgedetection Reset the edge detection rvcopyfromlvendo_Callback Copy RV from LV segmentation endocardium rvcopyfromlvepi_Callback Copy RV from LV segmentation epicardium 156 15 6 SEGMENTATION SUPERUNIT 15 6 6 Viability unit The purpose of the viability module is to quantify scar from delayed en hancement images The viability tools have been extensible described and validated in I and 12 The transmurality is documented in 13 The term noreflow that is used in the code is a legacy term since this was used in the scientfic literature at the time of implementation of the module instead of the now accepted term microvascular obstruction or MO There is no dedicated user interface all interactions are performed in the main window and some user changable defaults are displayed in the menu and stored in the SET struct Interactions The viability unit have interactions with the following units e Draw superunit The unit calls routines in the viability unit to perform
109. g corrections into account retrack_Callback This is called after manual corrections using both local and global effect 219 CHAPTER 15 UNIT IMPLEMENTATION v samplevelocity vx vy px py A c Sample velocity data v is vector with sampled velocity data Size is 2 nnodes x nframes segmentindex section no Divide the long axis of the heart into 7 segments according to AHAs 17 segment model segmentindex contain the index for the 7 different segments 2CH 1 basal anterior 2 mid anterior 3 apical anterior 4 apical inferior 5 mid inferior 6 basal inferior 7 apex 3CH 1 basal anteroseptal 2 mid anteroseptal 3 apical septal 4 apical lateral 5 mid inferolateral 6 basal inferolateral 7 apex 4CH 1 basal inferoseptal 2 mid inferoseptal 3 apical septal 4 apical lateral 5 mid anterolateral 6 basal anterolateral 7 apex segmentindex is a cellarray with length 7 Written by Helen Soneson 2008 09 29 Modified by Shruti and Einar after change in strain representation Modified by Einar to use dicom coordinates x setupdiffoperator no Dx Dy M tupdiffoperat This function is inspired by pdegrad but returns the operator matrix instead of actually calculating the gradient G setupmappingfunction no G is mapping from boundary functions to the entire domain The size of G is 2 nodes x 2 boundarynodes L setupmaterialoperator no Dx Dy M We will use the laplace operator for a start Calculate second derivative operato
110. g the dll files does is look for an open Segment this is done by looking for window names using Windows API It looks for windows that starts with Segment followed by space Note that this might need to be changed when renaming future products This check is done in pipe cpp The principle is that the plugin sends all DICOMs on the series level to the Segment process by the usage of pipes First a dummy DICOM is sent as preview file This was required for the old DICOM file loader The DICOMs to send is found by parsing the Sectra API and asking for images Please not there seems to be several bugs in the API that crasches Sectra This is documented in the code The challenge in the process is to convert data from Sectra API to usable DICOM files The documentation to the 204 15 9 FILE SUPERUNIT Sectra API is on their SDK and in this there is a Windows help file The SDK needs to be installed in order to be able to compile For details on how to compile the plugin please see Chapter The SDK is available from http userweb sectra se Username and password is documented in wiki SectraPlugin The name of the code and details needs to be same for 32 and 64 bit If both are registered then Sectra is able to automatically determine the correct version to run Interactions This unit calls the Openfile unit to load data from the Sectra PACS Datastructure No use of shared datastructure occurs Functions on Segmentside inits
111. ge view planes and imaging techniques written by Helen Soneson 2009 05 25 Moved by Nils Lundahl to maingui m 2012 07 20 Overloaded in RVQ GUI init g Create GUI initLogFile g Initiate log file initbullseye Autoselects slices with myocardium in them before GUI is opened Overloaded in Segment CMR GUI and Segment Spect GUI initmaingui g Initiates main GUI Overloaded in most other GUI s initmaintoolbar g This method is overloaded in any GUI with a toolbar varargout initopenfile g Initializes the openfile GUI Optional output is the fig Called by openfile main Overloaded in CVQgui doprotect initreportflow handles Overloaded in CVQgui inittoolbar g Initiates toolbars Overloaded in CVQgui 93 CHAPTER 15 UNIT IMPLEMENTATION loadguipositions g Load prestored positions of GUI s g maingui programversion Constructor Initialization of Segment GUI ok manualdraw_Buttonup_roi no xr yr slice Called by segment _main manualdraw _Buttonup Overloaded in CVQgui and RVQgui measure Buttonup g Button up function for measurements Overloaded in CVQgui stri lstr measureasklabel g Asks for a label of a measurement Overloaded in CVQgui and RVQgui measureclearall_Callback g Clear all measurements measureclearthis_Callback g arg Clear current measurement Overloaded in RVQgui measurefontsize g panel index Sets measure font size Used in CVQgui measurerenamethis_
112. geTypes A cell array contains the different precode image types in Segment They are e General e Perfusion Rest e Perfusion Stress e Strain FFE e Strain TFE e Late enhancement e Cine e Scout e Qflow e T2Stir e T1BB The image types are used among others to find what image stack is what for automated batch processing of files This list is subject to future changes 38 ImageViewPlanes ImagingTechniques ImagingTechniquesFiulNameses titles of the parameter files A cell array contains the different precode image view planes in Segment They are e 2CH e 3CH e 4CH e Sagittal e Coronal e Frontal e Transversal e Short axis e RVOT e Aorta e Pulmonalis e Vena cava inferior e Unspecified The image types are used among others to find what image stack is what for automated batch processing of files This list is subject to future changes Short names of the parameter files par This variable is created a startup Therefore Segment needs to be restarted before new parameter files can be used from the menu However the files themselves are not cached so the content in the files can be changed without restarting Segment See above for details 99 CHAPTER 12 DATA OBJECT ThisFrameOnly StartFrame SegIntersection IntersectionIM True if changes are applied only to the current timeframe Example of functionality is segmen tation clearing segmentation etc See detail
113. h endo and epi clearallrv_Callback Clear all rv segmentation both endo and epi clearslices no ind timeframes endo epi rvendo rvepi Workhorse in clearing slices clearslices_Callback endo epi rvendo rvepi Helper function to clear segmentation in selected slices clearslicesthis_Callback endo epi rvendo rvepi Clear segmentation for slices in this timeframe clearthis_Callback endo epi rvendo rvepi Helper function to clear segmentation in this current slice slice sourceslice destslice sourcetime desttime zdirsource zdirdest findmatch ingslices tono fromno doendo doepi dorvendo dorvepi takefromclosestseg Find matching slices between source image stack and destionation image stack The matching is based on camera position 155 CHAPTER 15 UNIT IMPLEMENTATION importsegmentation_Callback no Import segmentation from another image stack Imports to current image stack NO from no or if called with no input arguments user is asked desttimeframes destslices sourceslices importsegmentationhelper tono fromno doend Helper function to segmentimportsegmention Callback tono is destination of segmentation fromno is source The function is capable of handeling slice offsets and different pixelssizes as well as situations when number of timeframes differ When destination is not timeresolved and source is timeresolved then user is asked from what timeframe to take the segmentation from Work horse in importin
114. h the LV segmentation unit in Section 15 6 3 Interactions This unit calls the Helper functions superunit to handle mouse input from the user and the Draw superunit to make graphical updates It is related to the Contours unit described in Section 15 6 5 that are used to copy and import segmentations between image stacks The LV segmentation unit described in Section 15 6 3 shares code with the RV segmentation unit Datastructure The RV segmentation is stored in the SET variable and specifically the fields RVEndoX and RVEndoY The units are pixels Functions The functions are described in the file rv m This file is not autodocumented in this Technical manual since it contains propriety algorithms Please con sult the rv m files for details instead 15 6 5 Contours unit The purpose of the Contours unit is to do operations on segmentation con tours The unit is implemented in the file segmentation m 154 15 6 SEGMENTATION SUPERUNIT Interactions Since many of its operations change the segmentation this unit frequently calls Draw unit operations to update the graphic display Datastructure The segmentation information on which to operate is taken from the SET struct and the stack number is taken from NO variable Functions clear_helper Helper fcn to clear segmentation clearall_Callback Clear all segmentation both endo and epi lv and rv clearalllv_Callback silent Clear all lv segmentation bot
115. hat are not supported for other platforms than Windows even when running under Matlab one such feature is the PACS connection and the Segment server 18 5 Compiling documentation A script to update the entire documentation base is included Note that you need to have MikTex installed and properly configured prior to running this script When run from the main compilation script then the manuals are automatically uploaded to Medviso homepage The user or process specifies which software to document and the script creates the following documents provided that they are available for that software e Instructions for use The instructions for use are rebuilt with current data and version number taken from changelog m Depending on set tings the bibliography is also updated e Reference manual e Installation manual e Sectra PACS manual e Database manual e Technical manual Function definitions and help texts are extracted from a set of m files Note that therefore it is very important that the coding standard is closely followed on how to make help texts about functions Also all helper functions starting with the name my are automatically documented e Test report First validate callbacks are run to check if all callbacks are correct then the last result of maketest are used to build a test report e Test record e Release record 18 6 Sectra Plugin compilation You need to compile the Sectra Plugin in Microsoft Visual St
116. he SeriesDescription r getseriesnumber self Returns the Series Number z getsliceposition self Returns slice position r getslicethickness self Returns slicethickness r getspectspecialtag self Returns a special tag used in SPECT images r getstudyid self Returns study id field r getstudyuid self Returns the study instance uid r gettriggertime self Returns the trigger time of the image type gettype self Find the image type of a dicom image Old values for type is O mag 1 phase 2 Unknown 3 Unknown r getvelocityencodescale self Returns the VelocityEncodeScale field 188 15 9 FILE SUPERUNIT r getvenc self Returns the venc r getvencpos self Returns the vencpos Magnitude images get number 1 through plane flow gets number 2 The other directions are more tricky Philips and Siemens do it differently Velocity directions PhilipsVENC Siemens Flow Segment example SequenceName dir vencpos 1000 0 ends in rl RL L 2 0 1000 ends in ap AP P 3 o 0 100 ends in fh FH S 4 5525 ends in in Siemens datasets so far contain in ap and fh stacks The in stack is just through plane so we have to figure out which direction it is by looking at ImageOrientation haspixeldata self Checks to see that there is pixeldata r hasrepetitiontime self Returns the Repetition Time r
117. he optimal threshold value Toptim represent the optimal threshold for seperating the remote and the scar regions based on the existing scar seg mentation This value is defined by an exhaustive search where the threshold is set to all intensities represented in the image stack For each threshold the number of missclassified pixels are counted total of both missclassified remote pixels and missclassified scar pixels The optimal threshold value is then defined as the threshold corresponding to the minimal number of missclassified pixels 14 12 T2 T2 calculation implementation The signal intensity S in the images can be described with an exponential fit according to S K x e F2 Ts 11 72 14 12 T2 T2 CALCULATION IMPLEMENTATION where R is 1 T gt and K is an arbitrary constant In order to calculate the exponential fit one need at least three echo times in theory two would be enough but to ensure numerical stability Segment requires at least three points in time The curve fitting is solved by taking the logarithm woe Pee 12 where S is the signal intensity of the pixel R is 1 T2 Tg is the echo time and K is an arbitrary constant This equation is solved for each pixel withing the region of interest in a least square sense by standard direct nu merical method Finally the T gt value is calculated as 1 Ro In the litterature there are some evidence that a constant is advantageous in the fitting process 5
118. he smoothed T2 T2 value M is the map calculated in Equation 13 denotes pixel wise division C is the certainty map denotes convolution and F is the smoothing filter kernel 14 13 Longaxis volumes Volumes can be calculated using segmentation from longaxis images The algorithm begins with automatically locating images labeled 2CH 3CH and 4CH that contain segmentation If the same kind of segmentation is found in two such images the volume is calculated by rotating each segmentation area one full revolution around the axis of intersection and taking the mean of these volumes If there are three images that contain the same segmentation the volumes are calculated as described above for each pair of images and the mean of these three values is used 74 15 Unit Implementation This chapter contains the implementation of different units of Segment Some of the units are modules which means that they are a part of the program that represents a separate module and requires a special license file A unit is the smallest divided unit of the code documented in the technical manual 15 1 Main Segment superunit The purpose of the main Segment block is to work as a backbone for which all other units can be incorporated It hosts almost all central callbacks and motion functions The unit consists of the file segment_main m the GUI superclass maingui m and its software specific subclass This class hierarchy is documented in detail in
119. hen the center of the epicardial volume is used See Reference Manual for further details A logical array containing a 1 where the left ven tricle endocardial contour have been dragged Interpolation points for the endocardium Interpolation points for the endocardium X coordinates of endocardial pins Stored as a cell array of vectors of doubles with the size T x Z where T is the number of time frames and Z is the number of slices For more details about pins see the Reference Manual Y coordinates of endocardial pins Compact representation for endocardial pins Stored as a cell vector with the T elements con taining vectors See above 47 CHAPTER 13 SET VARIABLE EndoX EndoY EndoXView EndoYView EpiDraged EpilnterpX EpilnterpXView EpiPinX EpiPinXView EpiPinY EpiPinYView EpiX 48 X coordinates of the left ventricle endocardium Applied values are either or an array with size N xT x Z where N is the number of points along the contour 80 but technically DATA NumPoints T is the number of timeframes and Z is the num ber of slices Y coordinates of the endocardium A compact representation used for drawing the endocardial contour in montage view Stored as a double array with the size N 1 Z x T where N is the number of points along the contour DATA NumPoints T is the number of timeframes and Z is the number of slices It is the same as EndoX but each slice offseted and packe
120. ialize_struct r NUnserialize struct array doesn t mind shape write_tag mem tag_name vr data RWrites a dicom tag little endian explicit VR 196 15 9 FILE SUPERUNIT 15 9 4 Database unit The purpose of the patient database unit is to allow a simple access to both DICOM data and analysed mat files Interactions The data base is stored in a file called patientdatabase mat The location where the patient database is set in the preferences In the unit there is a timer that scans the index file and checks if that have been updated every 30 seconds It looks at a timestamp to prevent for loading the entire file In the same folder as where the patient database index file is stored there are three folders e Analysed this folder contains all mat files On the highest level there are folders with patient names In the second level there are the study date that each is a folder that contains mat files Characters that are not valid filename are removed by the function removeforbiddenchars m e DICOM this folder contains all DICOM files They are sorted into sub folders The files are sorted according to the following system where on the top level there are folders with patient name with an underscore and patient id i e ALF_A Bete_19730101010101 The names are con verted to only allow valid filename characters and spaces are changed to an underscore Removing forbidden characters are performed by the function removeforbi
121. icatetimeframes_Callback duplicates Removes duplicate timeframes askes for the number of duplicates Two means keep every second frame removenexttimeframes_Callback Remove next timeframe and upto and including last timeframe removeprevioustimeframes_Callback Removes previous timeframe and all frames to first timeframe removeselected_Callback Remove selected image stacks from current image stack removeslices_Callback ind force Remove slices from current image stack This is the workhorse when removing slices removethis_Callback Remove current slice 175 CHAPTER 15 UNIT IMPLEMENTATION removetimeframes ind Helper function to remove timeframes This is the workhorse when removing timeframes removeunselected_Callback Remove unselected slices from current image stack x resamplehelper f x Helper function to resample image stacks factor 2 gives x 2 x 0 5 factor 3 gives x 3x x 1 factor 4 gives x 4 x 1 5 factor 5 gives x 5 x 2 factor 2 5 gives x 2 5 x 1 factor 3 5 gives x 3 5 x 1 5 factor 0 5 gives x x 0 5 a odd 0 x 0 5 0 5 a even factor 0 5 gives x rotate90right_Callback Rotate current image stack 90 degrees right Currently not working properly setcolormap_Callback type Set colormap for current image stack setcurrenttimeframeasfirst Callback Sets current timeframe as first time frame by cycling data in time Works with existing contou
122. icknesstslicedist calclvvolumepolar no Calculate volume of lv when rotated image stacks no is the imsage stack The LV volume calculation includes longaxis compensation taken from the setting in the GUI and stored in the SET structure spacedist timedist calemmodedists no Calculate distances in space and time between mmode lines outim calcmontageviewim no matrix segmentedonly cmap c b im Calculate view image for montage view res calemyocardvolume numsectors no tf Calculate myocardvolume numsectors is the number of sectors to calculate in and no is the image stack uses findinmeansectorslice to do some of the calculation 106 15 3 CALCULATION SUPERUNIT xofs yofs calcoffset z type no panel Calculate offset required to plot coordinates in viewing mode specified by type cellx celly calcoffsetcells no panel type Same as calculateoffset but returns cells used in updatemodeldisplay impos ormat calcormat no Calculate orientation matrix for stack number no Can be used for coordinate transformations RLAPFH impos ormat XYZ 1 XYZ ormat RLAPFH impos 1 x y calcplaneintersections NO no TYPE type slice hslice Calculate intersections between image planes NO is the viewed plane no is the potentially intersecting plane TYPE is the viewtype of the viewed plane type is the viewtype of the intersecting plane slice is the slice of the intersecting plane hslice is the hori
123. ion e Make Segment CMR standalone make a standalone clinical MR edition executable e Make Segment CT standalone make a standalone clinical CT edition executable e Make CVQ standalone custom layout of Segment executable e Make RVQ standalone software adapted for kidney studies executable 237 CHAPTER 18 COMPILING SEGMENT e Make Matlab stubbed modules create a zip file of source code for release to the public e Make Matlab all modules but protected create a zip file of source code for trusted users only e Make Segment standalone with 4D flow make a standalone of Segment containing the 4D flow module for trusted users only Note You need to have Winzip self extractor installed on your computer to be able to run the standalone option The GUI also enables the user to select whether to run the test script before compiling making documentation and uploading the final compiled file to FTP It is necessary also to check that there are no critical tickets before compiling In some cases the combination of testing and compilation in one session fails To remedy this problem the function internaltools slowcompile was introduced Call this function with either segment or segmentcmr 18 3 Configuring Settings in the files are done in the section entitled mm HAH Settings EA Below you find a list of items that can be configured e Toolboxes used You need to manually enter all required toolboxes Thi
124. ions for mitralis and tricusp 15 5 9 Unwrap unit The purpose of the Unwrap unit is to provide the user with tools for per forming correction of wrapped phase values in phase contrast image stacks Interactions Interaction with the calculation unit to perform underlying calculations Datastructure The VENC information for flow analysis is taken from the VENC field of the SET struct The SET VENC field is updated by this unit 136 15 5 REPORT SUPERUNIT Functions applyandexitpushbutton_Callback Apply and Exit push button Saves the phase images to where they came from overwriting and using the VENC double relative the original autounwrappushbutton_Callback Perform automatic phase unwrapping on all flows cancelpushbutton_Callback Cancel pushbutton Exit window save nothing flows checkflowdata NO_to_check Check what flow data if any exists and return an array of stack numbers closewindow Everything that is common to the Apply and Exit and Cancel buttons flowdirectionlistbox_Callback Callback for the flow direction listbox pixel over_time getcurrentpixelovertime Returns the currently selected pixel over time in units of the N B ORIGINAL VENC tms getcurrenttime Returns the current time in ms slice getcurrentvelocityslice Returns the current velocity slice X Y getoverlayplotcoords Computes the coordinate vectors for the overlay plot Corners x 0 5 y 0 5
125. ject and aligns it to correct monitor 119 CHAPTER 15 UNIT IMPLEMENTATION 15 4 26 mymenu m MYMENU header options defaultstring MYMENU header item1 item2 item3 m m Same as menu but with the following additions more elegant uses keyboard to select items modal display can use default string last optional argument is figure handle 15 4 27 mymkdir m MYMKDIR NEWDIR SUCESS MYMKDIR NEWDIR Make directory difference to MKDIR is that is does not issue an error message if the folder already exists See also MYCOPY MKDIR 15 4 28 mymovefile m STATUS MESSAGE MESSAGEID MOVEFILE SOURCE DESTINATION MODE moves the file in source to dest Essentially a wrapper for MOVEFILE kept for naming consistency See also MYCOPYFILE MOVEFILE 15 4 29 mymsgbox m MYMSGBOX Helper function works as MSGBOX MYMSGBOX STRI TITLE ALIGNMENT STRI String to display TITLE Title of messagebox FIGHANDLE Optional figure handle indicating alignment 120 15 4 HELPER FUNCTIONS SUPERUNIT See also MYWARNING MYMSGBOX MYADJUST MYWAITBARSTART 15 4 30 myoptimpartial m Script for exhaustive search 15 4 31 myrequirepc m Z MYREQUIREPC Returns true if PC platform If not PC platform then an error messsage is displayed Used to block certain functions that is not implemented for other platforms than PC 15 4 32 myset m MYSET Same as SET but removes NaN s in the handles
126. k for changing to next time frame play_Callback Callback for play togglebutton prev_Callback Callback for changing to previous time frame sectorrotation_Callback Show handle for sector rotation sectorrotationslider_Callback Rotate sector 223 CHAPTER 15 UNIT IMPLEMENTATION sliceslider_Callback Callback for slider to toggle slice timebar_ButtonDownFcn hObject Buttondown function for graphical timebar object Activates dragging of timebars timebaraxes_ButtonDownFcn hObject Buttondown function for timebar axes Changes current timeframe to the one closest to position of clicked point timebaraxes_ButtonUpFcn hObject Buttonup function for timebar axes of image specified by input parameter field Deactivates dragging of timebar timebaraxes MotionFen tbobj no Mouse motion function for timebar axes of image specified by input parameter field Used for dragging timebars to change current timeframe or start end points of timeframes in which to align images translatecontour Callback direction Translate segmentation contours in all image stack views translategrid_Callback direction Translate grid in tagging image updateimages Update all image stacks and also timebar updateplot Plot strain in axes updatetimebar Update timebar axis viewparameter_Callback Callback from listbox selection of parameter to plot 15 10 5 MPR unit The purpose of the MPR unit is to do m
127. l drawimageview nos sz panelstype Draws a full view specified by the arguments drawinterp no panel olshow Initiate handles and draw interpolation points Do not work well with overlays drawintersectionpoints no panel Initiate handles and draw intersections with other contours drawintersections Draw intersections between image visible stacks Uses calcplaneintersection to calculate intersection lines This function respects view settings drawmarhelper no panel Function to draw MaR contour on screeen used from drawimageslice drawimagemontage drawmeasures no panel Draw measurements if available drawmontagecontours no panel Initiate handles and draw contours for montage view drawmontageimagetypetext no pno panel Initiate handles and draw image type text drawmontageinterp no panel Initiate handles and draw interpolation points for montage view drawmontagemeasures no panel Initiate handles and draw measurements for montage view drawmontagepins no panel Initiate handles and draw pins for montage view drawmontagepoints no panel Initiate handles and draw annotation points for montage view 102 15 2 DRAW SUPERUNIT drawpins no panel Initiate handles and draw pins drawsliceno no Call updatenopanels drawthumbnailframes Draw frames around thumbnail images drawthumbnails calculatepreview sliderupdated Draw all thumbnails Calculatepreview is a boolean indicating if thumbnails need
128. l bar SegmentFolder Location of the folder from which Segmentis loaded imagedescriptionfilext document for setting image description pa rameters 36 manualfile GUI GUISettings GUIPositions AllowInt16 Pref PrefHandles Location of the Reference manual Structure of mygui objects for windows that use this class GUI settings Struct array to store the positions of GUI s that have been in use Option whether or not to allow int16 data Structure with preferences For further details please see Section 15 7 2 Handles for Preferences window PrefHandlesAdvancefilandles for Advanced Preferences window PrefHandlesPacs Preview StartTime Run Record LastPointer Handles for PACS Preferences window Struct storing preview data This struct is in tensely used by the file open GUI Generally the data is store in this struct and thereafter copied to the SET variable upon completion of the loading process Therefore this struct also contains infor mation on the last loaded viewed image stack Start time for video playback True if a movie is playing True if recording is active in the movie recorder GUI Type of the pointer displayed LastPointerShapeCD amp tdata of shape of the pointer displayed 37 CHAPTER 12 DATA OBJECT VisibleThumbnails Array of indices of thumbnails visible in main GUI Icons Structure of images used as icons in toolbars and icon bars Ima
129. l image stacks viewhidecolorbar_Callback Toggle visibility of colorbar viewhideimagestack_Callback no Remove clicked image stack from view panels viewhideinterp_Callback varargin Toggle visibility of contours from other image stacks viewhideintersections_Callback varargin Toggle visibility of plane intersections viewhidelv_Callback varargin Toggle visibility of lv segmentation viewhidemanualinteraction_Callback toogle visibility of manual interaction of Scar MaR viewhidemar_Callback varargin Toggle visibility of MaR contours viewhidemeasures_Callback Toggle visibility of measurements viewhideothercontour_Callback varargin Toggle visibility of contours from other image stacks 89 CHAPTER 15 UNIT IMPLEMENTATION viewhidepanel_Callback Hides current panel viewhidepap_Callback Toggle visibility of papillary overlay viewhidepins_Callback varargin Toggle visibility of pins viewhideplus_Callback varargin Toggle visibility of center viewhidepoints_Callback Toggle visibility of annotation points viewhideroi_Callback varargin Toggle visibility of roi s viewhiderv_Callback varargin Toggle visibility of rv segmentation viewhidescar_Callback varargin Toggle visibility of scar contours viewhidetext_Callback varargin Toggle visibility of text viewimage_Callback type Select type of image to view on screen viewimagestack_Callback no Make clicked image stack visible
130. l naming conventions apply 6 4 Text edit boxes ends with edit Static text ends with text Axes objects ends with axes Pushbuttons ends with pushbutton Radiobuttons ends with radiobutton Checkboxes ends with checkbox Togglebuttons ends with checkbox Object oriented programming For new objected oriented functions the new syntax introduced in Mat lab R2007b should be used The old usage where the class definition is stored in a separate folder is obsoloted and existing code will be rewritten to new standard Note that this new coding methods using classdef requires that an end statement is inserted in the end of the method code 14 6 5 PACKAGING 6 5 Packaging To improve the file structure Matlab s packaging feature is used Files that are part of the same module are placed in a directory named with an initial sign Calling a function file fcn_name m from a package package_name is done by entering package_name fcn_name without the When adding packaged files to the compilation process the full directory name must be in cluded in the string In the example above this becomes package_name filesep fcn_name m 6 6 General coding conventions The use of boolean variables in function calls should be avoided since this significantly decreases code readability This is especially true in API close functions Instead it is suggested to write two functions with different names that performes the diffe
131. lcmean segmentindex data calculate all segments meanvalue at every timestep varible data is the parameter to calculate the mean over 214 15 10 ANALYSIS SUPERUNIT addicon_helper callback tooltip cdata tag separator Helper function to add an icon P pos addlocal_helper P pos arclen localangles radx rady shearx sheary outx outy xind yind Helper function to add local basis functions xnew ynew anatomical2straincoords x y Convert from anatimical coordinates to strain coordinates anatomicalcorrectionpoint_Buttonup This is called on mouse up anatomicalcorrectionpoint_Motion This function is called when user moves the point anatomicalcorrectionpoints_Buttondown Called when click on correction point in anatomical image 1 arclength x y Returns arclength of a curve p1 p2 gm avpointsfinderhelper dc Finds two peaks p1 p2 of a signal dc gm is a goodness measure bullseye_Callback Plots bullseys plot of strain data alpha arclen calcalpha no centerx centery Calculates the localangle for boundary node x y is boundary points alpha is angle between normal and x axis arclen is arclength in longaxis direction calcandview_Callback Calculate strain in one long axis image and open the strain gui inside calcinside no inside x y Calculates which points are inside of centerline raddist calcraddist x y centerx centery Calculates radialdistance to node points x y given the centerline centerx c
132. lds Brightness and Contrast translates into intensity according to the equation I cx b 0 5 1 where c is contrast b is brightness x is the input intensity and J is the output remapped intensity The intensity is then clipped to the range 0 1 The field Compression is reserved for future use and will be used to implement image mappings that are sigmoid shaped The fields IntensityScaling and IntensityOffset are used to convert the image data IM to the true data as presented in the DICOM images The true data is calculated as z la 8 2 where z is the true image data J is the data stored in the field IM a is IntensityScaling and IntensityOffset See above See above Inversion time in MRI pulse sequence Read from DICOM tags if presented otherwise set to zero Given in milliseconds LVM LVV LevelSet Linked Longaxis MaR Measure Mmodex Mmodey Mmodelx Mmodely Mmodemi Mmodem2 The left ventricle myocardial volume is calculated as EPV LVV PV Unit is ml The volume within the left ventricular endo cardium Unit is ml Struct that contains general object segmentation module List of numbers of image stacks that are linked to this stack in Parent Children relations Long axis motion of the left ventricle see Refer ence Manual for details on how the volume is com pensated for long axis motion To convert to mm subtract with 1 Struct that contains automatic and or m
133. led when clicked puts an pin and refines dragepi_Buttondown type panel Button down function for scaling of objects contours dragepi Buttonup type Button up function for scaling dragepi_Motion reset Motion function for scaling 77 CHAPTER 15 UNIT IMPLEMENTATION ok enablecalculation Returns ok if slices are selected Sideeffect of this function is that it turns on interaction lock stops movie Calling this function will not allow user to click on a new function before endoffcalculation is called Note that this mechanism needs to be pretty safe with try catch clauses otherwise Segment may hang Viewrefresh calls endoffcalculation endo_Buttondown panel Button down function for manual draw of endocardium endoffcalculation Turns off interaction lock called after a calculation See above epi_Buttondown panel Button down function for manual draw of endocardium esed_Buttondown type Buttondown function when dragging ES or ED markers esed_Buttonup type Buttonup function when dragging ES or ED markers esed_Motion type Motion function when dragging ES or ED markers in volume graph evalcommand_Callback Function to evaluate matlab commands from compiled version fasterframerate_Callback Makes movie play faster figure_DeleteFcn Shut down Segment in a controlled manner and remove global DATA SET NO Note that filequit callback takes care of asking user yesno preview genemptypreview datap
134. lementation of the External PACS plugin and a standalone application that is called when data is sent from the external PACS system starts Segment if not already open and sends instructions to it on what data to open The Segment side imple mentation consists of a timed function that repeatedly checks for incoming data from the standalone application Interactions This unit calls the Openfile and Patient Database units to load data from the external PACS Datastructure No use of shared datastructure occurs Functions varargout externalpacs varargin Switchyard for EXTERNALPACS module 206 15 10 ANALYSIS SUPERUNIT initexternalpacs Starts the EXTERNALPACSTIMER The timer executes function loadexternalpacs every second loadexternalpacs Load files from EXTERNALPACS pacs stopexternalpacs Stops the EXTERNALPACSTIMER if it s running 15 10 Analysis superunit The Analysis superunit contains functions for performing special kinds of analysis on image stacks 15 10 1 T2 unit The purpose of the T2 unit is to do analysis of T2 image stacks Interactions This unit uses the Calculation superunit mainly to do calculations of T2 maps Datastructure The image information on which to operate is taken from the SET struct and the stack number is taken from NO variable SET is also used for storing the derived T2 maps Functions addiconhelper callback tooltip cdata tag separator Helper fcn to add an icon
135. ly Segment uses a coordi nate system x y z that is relative to the respective image stack In other words for each image stack the relations between RL AP FH and x y z is different Throughout the program the x dimension refers to the first dimension along the arrays i e the rows in Matlab The upper left pixel in the images dis played on the screen have the coordinate 1 1 The unit used is in pixels In the normal image coordinate system this means what is usually meant as the y coordinate if one thinks of coordinate systems learned in elementary school For instance plotting commands therefore generally takes the form plot SET NO EndoY 3 1 SET NO EndoX 3 1 This will plot the contour of the endocardium of the third time frame and the first slice of the current image stack The upper left most slice in the montage view is slice one Furthermore it is assumed that the slices should be ordered so that going from the first slice to the last would be going from the base to the apex of the heart The relations between the x y z and RL AP FH coordinate systems is given by the fields ImagePosition and ImageOrientation Below are two examples given The RL AP FH coordinates center of the voxel s SET 1 1M 1 1 1 are given by SET 1 ImagePosition The RL AP FH coordinates center of the voxel SET 1 IM 2 3 4 are 19 CHAPTER 7 COORDINATE SYSTEMS given by zdir cross SET 1 Image0rientation 1
136. me that should appear in Segment menu is expected Currently there are two other plugins that are shipped with the standard Segment edition e plugin_imageloader m Plugin to load non DICOM images into Seg ment This plugin can load for instance jpg bmp tif png files into Segment This plugin gives some elementary details on the internal data structure e plugin_calibrate m Plugin to calibrate image resolution This plu gin gives some hints on using own GUI s and also some details about the internal data structure in Segment e plugin_template m Template plugin simple template for creating plugins e plugin_summarize m Plugin to summarize results from multiple mat files This function is useful to read when creating own export scripts e plugin_phaseflow m Plugin to enable to make flow measurement when there is only phase images available For further documentation of the two first plug ins please see the Segment User Manual 243 20 Segment User Community As a result of the growing interest in Segment and as a response of numerous requests Medviso AB has started to form a user community web place This initiative will be enlarged significantly as the members of the community both requests more and also expands the community It is worth noting that in the user survey spring 2010 out of 169 answers 147 answered that they would follow the user community and 45 answered that they would follow it often A prelimi
137. measurements to report addflowanalysis report floop dohtml Add flow analysis from image stack floop to report addfreetext report Add free text patient evaluation to report stri addimagesax report Add shortaxis image to report 141 CHAPTER 15 UNIT IMPLEMENTATION strlax addimageslax report Add table of longaxis images to report addlvanalysis report dohtml Add LV analysis to report addmaranalysis report dohtml Add MaR analysis to report addpatientdata report Add patient demographics to report addperfusion report Add perfusion analysis to report addrvanalysis report Add RV analysis to report addscaranalysis report dohtml Add scar analysis to report addscreenshot report Add screenshot image s to report addshuntvalveanalysis report Add Qp Qs and Shunt and Valve analysis to report addt2star report Add T2 analysis image to report addwallthickness report Add wallthickness analysis to report age calcage AcqDate BirthDate calculate patient age by using Aqcuisition date and Birth date close_Callback Close reportsheet GUI distance_Callback Callback from distance measurements checkbox 142 15 5 REPORT SUPERUNIT flowanalysis_Callback Callback from flow analysis checkbox generatereport_Callback arg This is the main function that actually makes the report valuecells outlier generatevaluecells value refvalues Creates data cells used for LV
138. method updateprefhandlesadvanced g Make update of handles in advanced preferences GUI out viabilityallowweighted Return whether to allow weighted viability mode Functions in maingui m defaultpref g Sets Pref to default values Overloads method in main GUI dispwelcometext g Displays welcome text Overloaded in CVQgui SegmentCMR GUI 98 15 1 MAIN SEGMENT SUPERUNIT fileopen_Callback g Loads a set of files as a 4D volume and also updates preferences Calls the fcn openfile which displays the fileloader GUI Overloaded in CVQgui filesaveallas_Callback g pathname filename savetodatabase true here should be a switch case clause on set preferences for save to hlocal disk or patientdatabase if savetodatabase initLogFile g Initiate log file Overloads main GUI method initbullseye Autoselects slices with myocardium in them before GUI is opened initmaingui g Initiates main GUI Overload SegmentGUI method to use CMR gui instead initmaintoolbar g Intialization of main toolbar If new handles are added add these to list in killhandles m as well inittoolbar g Initiates toolbars Create menubar licensemsg Overloads SegmentGUI method g segmentmrgui programversion Constructor tip singleframetip Return tip for single frame mode updateicons g mode Updates icons when new mode is selected Overloads method in main GUI If making major changes make sure to update csegm
139. mmodempoint1_Motion Motion function for mmodepoint one mmodempoint2_Motion Motion function for mmodepoint two mmodepoint1_Buttondown panel Called when mmodepointi is pressed down sets motion and buttonup function mmodepoint2_Buttondown panel Called when mmodepointi is pressed down sets motion and buttonup function 82 15 1 MAIN SEGMENT SUPERUNIT mmodetimebar1_Buttondown panel Called when mmodepointi is pressed down sets motion and buttonup function mmodetimebar1_ Motion Motion function for mmodepoint timebar mmodetimebar2_Buttondown panel Called when mmodepoint1 is pressed down sets motion and buttonup function mmodetimebar2_Motion Motion function for mmodepoint timebar montage Buttondown panel Button down function for selecting slices in montage view montage_Buttonup panel Button up fucntion for selecting slices in montage view montage_Motion Motion function when selection slices in montage view move_Buttondown type panel Button down function for moving translating objects contours move Buttonup type Button up function for moving functions move_Motion reset Motion function for moving translating objects contours movealltowardsapex_Callback Changes CurrentSlice and that of parallel image stacks towards apex movealltowardsbase_Callback Changes CurrentSlice and that of parallel image stacks towards base movetowardsapex_Callback Change current slice towards
140. mplate roitemplatesetlabel_Callback Function to rename roi by template roithresholdnumeric_Callback numeric threshhold inspector roithresholdvisual_Callback visual threshhold inspector roitoendo_Callback Copy from endocardium to a ROI roivisualslider_Callback arg gui for visual threshhold roivisualsliderkeypressed key pressed function for visual slider selectroi_Buttondown panel roinbr Buttondown function used for changing current ROI 15 7 Resources superunit This superunit contains functions called by the user and whose interactions with other functions are few 15 7 1 Help unit The purpose of the Help unit is to contain functions that are called from the Help menu Interactions Interactions are negligible from this unit 167 CHAPTER 15 UNIT IMPLEMENTATION Datastructure Use of datastructures is negligible Functions about_Callback Displays help information about the software aboutrvq_Callback Displays help information about RVQ bug_Callback User bug report function generalhelp_Callback Open Medviso homepage in browser hotkeys_Callback Shows help of hot keys in Segment instructionsforuse_Callback Open instructions for use file openlogfiles_Callback Open list of log files in browser openthislogfile_Callback Open log file for this session in browser support_Callback Open mail composer to submitt email to support supportreq_Callback call Callback to
141. n and spectmarsegmentation for the automatic seg mentation in t2w CMR respectively SPECT 162 15 6 SEGMENTATION SUPERUNIT 15 6 8 ROI analysis unit The purpose of the ROI analysis unit is to provide general tools for region of interest analysis and to be able to extract signal intensities and related statistics Interactions e Draw superunit since it is responsible to graphically draw the regions of interest on screen e Report superunit uses the export to clipboard features to export data e The report unit uses the calctruedata function in the Calculation superunit Datastructure The data is stored in the SET variable in the field Roi and contains the following fields e X X coordinates of regions of interests They are stored in an array as N x T where N is the number of points along the contour to be precise it is actually DATA NumPoints T is the number of time frames For non time resolved ROPs X can also be a vector of length N e Y Y coordinates of regions of interest For details about size see above e T T coordinates of the region of interest e Z Z coordinate of the region of interest e Sign sign of the region of interest This is used for flow quantifications and is stored as a vector with elements that are either 1 or 1 e Name name of the region of interest e LineSpec line specification for the region of interests Stored as a string as Matlab compatible line specifications Examples are
142. nal structure of the File function superunit and transaction analysis 179 CHAPTER 15 UNIT IMPLEMENTATION Datastructure The function heavily use the DATA Preview field for communication with the segment main in the loading process Functions This subsection describes the subfunctions of openfile m bothmagnitudeandphase no Called when image stack contains both magnitude and phase browsebutton_Callback Callback when user wants to browse for new folder cancelpushbutton_Callback Dismiss the figure continueloading This function is called from cropbox buttondown It continues to load the whole images stack and finally call Segment to tell that finished loading one image stack cropbox Called from continue loading and sets up GUI to ask user to select region of interest to load cropbox_buttondown Buttondown function for crop This is equal to select cropbox_motion Motion function for cropbox enablesegmentgui no Helper function that enables vital GUI options in main gui exitgui Quits and exits the gui factor_Callback Help function to split number of selected frames in to prime numbers 180 15 9 FILE SUPERUNIT filtercheckbox_Callback This refreshes and thus enables filtering to be displayed z getfilenumber stri Take only the last digits of a filename if numbers exist files2load getfiles2load ind2load Gets files to load as a cell removes chache files dicom dirs seg files etc
143. names Check functional groups to see if they are implicit createnewtags self Create a new struct of tags r getaccessionnumber self Returns the accessionnumber field r getacquisitiontime self Returns the Acquisition Time r getbitsstored self Returns the BitsStored field 185 CHAPTER 15 UNIT IMPLEMENTATION r getechotime self Returns the Echo Time r getflipangle self Returns the FlipAngle field images getimages self Return the images contained in the dicom file The return data will be a struct with the fields im The pixeldata as NxM single matrix gt spacetimepos the position of the image in space and time triggertime The trigger time of the image instancenumber The instance number of the image multiframenumber The position in PixelData buffer of the image images getimagesframetime self nFrames Used by get images when numberofframes are greater then one and the frame incremental pointer is set to frametime images getimagesmultirrtimeslice self nFrames Used by get images when numberofframes are greater then one and the frame incremental pointer is set to rr timeslice images getimagesmultislice self nFrames Used by getimages as a default multiframe parser images getimagessingleframe self Used by get images when there is only one frame r getimagetype self Returns the image type r getinstancenumber self Returns the instance n
144. nary start page of the user community can be found on the following Facebook page http www facebook com pages Segment 119840021370285 It is the aim to be able to provide the following activities on the user com munity pages 1 Participate in discussion forums Currently forums for Developers dis cussion and tips and tricks Feature requests Segment and Mac 2 Contribute and share own plug ins This feature is currently not avail able If you have plug ins that you want to share please email them to support medviso com and we will manually upload the plug in Currently writing own plug ins to Segment is documented in the Seg ment Technical Manual 3 FAQ sections Currently we are gathering FAQ in our support program All or almost all support request will be made available in a searchable data base Exceptions on when support requests are not included when the user request so in conjunction with classified projects Staff from Medviso AB will follow the user community page closely and mon itor any incoming questions or uprising discussions If you have any ideas or suggestions on how we should improve the user community please send us an email to support medviso com 245 Bibliography 1 E Heiberg J Sjogren M Ugander M Carlsson H Engblom and H Arheden Design and validation of Segment freely available software for cardiovascular image analysis BMC Med Imaging 10 1 2010 E Heiberg Automated Featur
145. ncropped image data The fields OrgYSize OrgTSize and OrgZSize have the same function in the other coordinate directions Original filename Note that this information is removed when anonymizing an image stack Number of an image stack that is currently used as a color overlay of this stack Left ventricular peak ejection rate Taken as the largest negative derivative of LVV Time of peak ejection Given in time frames PFR PFRT PV PapillaryIM Parent PathName Left ventricle peak filling rate Calculated us ing circular convolution with a central difference three elements and taken as the largest deriva tive of LVV Time of peak filling Given in time frames Volume of the papillary muscles See Reference Manual for further details how that is calculated Visualisation of papillaries to overlay on image Number of the image stack from which this stack was derived Path to where the image is saved 59 CHAPTER 13 SET VARIABLE PatientiInfo Perfusion Point ProgramVersion RVEDV 60 e Name is the name of the patient e ID is the PatientID e BirthDate in the date format YYYYMMDD e Sex Applied values are M F e Age Applied values are numeric gt 78Y e HeartRate Same as SET NO HeartRate retained for backwards compability e AcquisitionDate Applied values and YYYYMMDD e BSA Applied values 0 or numeric value
146. nctions to do the work wallthickness calcwallthickness sectors no Calculate wallthickness Uses calcendoradius and calcepiradius to do the work window level con2win contrast brightness no Convert from contrast to window and level x y z cyl2cart xin yin slice numslices rotationcenter Convert from cylindrical to cartesian coordinates z econvn im f Function to filter image uses fastest available convolver res varargout findmeaninsector type inp pos numsectors no tf Find indicies of points along the contour that corresponds to which sector Then also calculated mean values of the input inp varargout findmeaninsectorslice type numpoints tf slice numsectors no endox endoy epix epiy rotation Find indicies of points along the contour that corresponds to which sector Used when analysing the myocardium of short axis slices Operates on given slice 108 15 3 CALCULATION SUPERUNIT pos xdir ydir zdir getimageposandorientation no slice type Return image orientation for current slice or second input argument If two outputvariables then zdir is also outputed x y z gla2sax xi yi no Convert image coordinates from GLA to short axis view z remapuint8 varargin Same as remapuint8viewim but squeezes result to make sure it can be viewed other than in the main window z remapuint8viewim im no tempmap c b If SET no Colormap exists Remap from image data to true color using color lookup
147. new ynew innersurface x y no dist Takes a surface x y and returns a new surface inside of this surface with a distance of dist mm x are assumed to be size NumDataPoints Z x y meshfixer x y Fix a mesh if the layers are twisted The mesh is assumed to be rows of coordinates mmodemeasurements_Callback Export mmode measurements screenshot _Callback Create an image file of a screenshot of the main axis 15 6 Segmentation superunit The Segmentation superunit contains functions that are used for doing seg mentations on images These are used to perform quantifications and usually leave visible traces that require graphical updates performed by the Draw su perunit 15 6 1 Measurement unit The purpose of the Measurement unit is to make linear measurements of details in images Some of these measurements can be used for other quan tifications Interactions This unit calls the Helper functions superunit to handle mouse input from the user and the Draw superunit to make graphical updates Datastructure The SET struct has a field Measure which is a struct that contains measure ments in the image stack If no measures exist then Measure is an empty array If measures exist then it is a structure array where each measurement has the following fields e XA 2x1 vector with X coordinates 150 15 6 SEGMENTATION SUPERUNIT e Y A 2x1 vector with Y coordinates e Z scalar with the slice Length Length of the mea
148. nt like software the subclass segmentmakeitclass is used This subclass is used for the compilation of the standalone research edition of Segment and is further divided into subclasses such as segmentcmrmakeitclass for compilation of cardiac MR clinical edi tion Segment CMR segmentctmakeitclass for compilation of cardiac CT clinical edition Segment CT and segmentmakematlabclass for packaging 31 CHAPTER 11 CLASS HIERARCHY OVERVIEW the source code cardiac research edition An overview is provided in Fig ure 3 Makeit superclass Segment Makeit subclass Other Makeit subclasses not documented here Segment Segment CMR Segment CT inde iii Makematlab subclass Makeit subclass Makeit subclass not documented here Figure 3 Overview of the class hierarchy of the compilation process 32 12 DATA Object This global object is an instance to the class segmentgui It contains meth ods and properties that are used to store properties and access the graphical handles preferences etc It is an instance of one of the subclasses of the maingui class and contains the following properties LogFile ProgramVersion ProgramName fig BlockingFigs imagefig DataLoaded Silent Handles InteractionLock Location of the log file keeping track of the current session A string containing the version number This string is initiated at startup Name of the program in use e g Segm
149. odule interacts with the DATA Preview field in the exact same way as the standard file loader does 16 1 2 Datastructure It uses the structure in DATA Preview to store information and pass on to code to set up SET structure 16 1 3 Functions The documentation for the usage of the Bruker Module is given in Segment User Manual 16 2 MIP module MIP stands for maximum intensity projection The MIP module is still a work in progress module 16 2 1 Interactions No interactions besides usage of SET and NO to retreive image data 16 2 2 Datastructure Will be documented when fully functional 16 2 3 Functions Will be documented when fully functional 233 CHAPTER 16 MODULE IMPLEMENTATION 16 3 Corelab module The purpose of the Corelab Module is to implement support for working with Segment in a Corelab setting 16 3 1 Interactions The interactions are performed only with Medviso AB corelab database Transfer and local file system for downloaded image files 16 3 2 Datastructure Not applicable 16 3 3 Functions For internal use only and no public documentation will be made available 234 17 Testing Segment To ensure highest quality of Segment as possible a complete software testing system has been implemented The test procedures include both system integration tests as well as unit implementation tests The automated testing system produces a comprehensive test report testreport tex including found
150. om file Serialize data arg and mem create_chunk indata ESerializes a 1xn cell array of uint8 1xn arrays str create_chunk_va varargin Avarargin shortcut to create_chunk r create_metaheader instance_uid EReturns a memorybasket containing a dicom r generate uid EReturns a new random UID uses the matlab root UID 195 CHAPTER 15 UNIT IMPLEMENTATION tags get_tags EReturns a tags struct with tag names as fieldnames and tag as value tag name_to_tag name OConvert a tag name to a tag outdata parse_chunk data NInverse of create_chunk varargout parse_chunk_va data Avarargout shortcut to parse_chunk stri secondtostring t Nonverts from seconds to a timestring with hhmmss sss r serialize data ESerializes a matlab variable Return a 1xn uint8 array r serialize_cell data ESerialize a cell array doesn t mind shape r serialize_char data ESerialize a char array doesn t mind shape r serialize_logical data ESerialize a logical array doesn t mind shape r serialize_struct data ESerialize a struct array doesn t mind shape data unserialize r NUnserialize 1xn uint8 array r to a matlab variable data unserialize_cell r NUnserialize a cell array doesn t mind shape data unserialize_char r NUnserialize a char array doesn t mind shape data unserialize_logical r NUnserialize a logical array doesn t mind shape data unser
151. onal and indicates alignment See also MYWAITBARUPDATE MYWAITBARCLOSE 15 4 43 mywaitbarupdate m H MYWAITBARDATE H Update a mywaitbarstructure and increment counter one step Graphic is updated depends on setting when intializing the structure 123 CHAPTER 15 UNIT IMPLEMENTATION See also MYWAITBARSTART MYWAITBARCLOSE 15 4 44 mywarning m MYWARNING STRI HANDLE Displays a warning message User needs to click OK to discard message See also MYWARNINGNOBLOCK 15 4 45 mywarningnoblock m MYWARNING STRI HANDLE Displays a warning message User needs to click OK to discard message See also MYWARNINGNOBLOCK 15 4 46 myworkoff m MYWORKOFF Graphically show that calculation is finished by restoring pointer 15 4 47 myworkon m MYWORKON Graphically indicate that Segment is busy by showing watch pointer 15 5 Report superunit The Report superunit contains functions that report data to the user Some of these functions are of higher order and use others to extract data to be used as a subreport An overview of the units and how they communicate is provided in Figure 15 5 1 Report 3D unit The purpose of the Report 3D unit is to do 3D model reports Interactions The Export unit is called for export of data 124 15 5 REPORT SUPERUNIT Pulse Wave Velocity Qp Qs Valve Report Sheet Report Bullseye Report Slice Report Radvel Report Volume Report 3D
152. only one frame return 0 If one can t find any triggertime information return 1000 nFrames 1 that is totaltime should be 1 second r sortind gettimevector self tsize Return time vector from acquisiontimes if available r getvenc self Return venc if all images agree or some images agree and other specify zero Else throw error r hascollisions self imbase offset Returns true if two images in the object gets the same coordinates using imbase and offset stri hascollisionshelper self impos Returns error message with appropriate slice distances r hasrepetitiontime self Return true if all dicom files has repetition time r hastriggertime self Returns true if all dicom files has trigger time r ismatch self dicom Check if a dicom files has the same line as all dicom files should have in this stack 193 CHAPTER 15 UNIT IMPLEMENTATION base offset makeimbase self dimsizes Return a base for the loaded image stack im makeimdata self imbase offset dimsizes cropbox OCombines all images in the stack to an im suitable for SET im r render self datapath cropbox Renders the dicom files and images in this stack to a preview and set struct suitable for passing on to segment m If cropbox load entire image self segrawstack line Constuctor Initiate all properties setdicoms self dicoms Takes a list of segdicomtags objects and saves them in self dicoms Also s
153. ontal Transversal Short axis gt RVOT Aorta Pulmonalis Vena cava inferior ImagingTechnique String of capital letters identifying type acquisi tion used when acquiring the image stack Possible values depends are given by the par files Each such files corresponds to one image type and con tains information of how image should be mapped before segmentation The two first letters should correspond to imaging modality i e MR CT PT US CR Shipped par files are CTheart par Segmentation of LV MRBB par MR black blood sequence MRDE par MR delayed contrast enhance ment MRGE par MR gradient echo images MRPDW par MR proton density weighted im ages MRSSFP par MR steady state free precision or fiesta MRSTIR par MR STIR pulse sequence edema sequence MRTOF par MR Time of flight sequence for vessels NMBPSPECT par Blood pool SPECT im ages OT par Myocardial probability obsoleted PT par Generic for PET not for segmenta tion use US par Generic for ultrasound Not for seg mentation use 99 CHAPTER 13 SET VARIABLE 56 IntensityMapping IntensityScaling IntensityO0ffset IntensityScaling InversionTime A struct containing information how the voxel val ues of the image stack is shown on the screen The struct has the following fields e Brightness e Contrast e Compression Reserved for future use The fie
154. open support request GUI tutorials_Callback Opens the webpage for showing tutorials on the software usermanual_Callback Open reference manual 168 15 7 RESOURCES SUPERUNIT 15 7 2 Preferences unit The purpose of the preferences unit is to provide a mechanism of storing user preferences in Segment For a complete description of the preferences and their usage see the Refer ence Manual The preferences are read when Segment is started or when the preferences GUI are opened Segment tries to find a suitable place for the preferences file by looking in the environment variables APPDATA USERPROFILE HOMEPATH Place can be found by calling the Segment func tion getpreferencespath Interactions The preferences data is read from multiple places in Segment but is only assigned in segpref m with the exception of loading that sets latest loaded file Datastructure The preferences are stored in the DATA object with the fields e datapath Path to image data This is the path first opened when the fileloader GUI is started e exportpath Path where image data is exported to e AnonymMode True if patient details should no be shown on screen Note that this does only affect the screen To permanently anonymize an image stack see Reference Manual for details e AddPoints True if pins should be added when manually drawing a part of a contour e EndoCenter True if the center of the endocardium is used for drawing spikes
155. or each point e Z 1 x N vector with slice i e one for each point e Label 1 x N cell array with string with the labels Originally all points were non time resolved Thereafter where time resolved points implemented by making T points from one point Non time resolved points are shown as bold text Time resolved points are only implicitly con nected by their position and more importantly the label Functions point_Buttonup Button up function for points point_Motion Motion function for points pointat_Buttondown panel type Buttondown function when clicked at a point pointclearall Clear all points pointclearall_Callback Clear all points pointcleartemplate_Callback Clear points using naming template pointdeletethis_Callback Delete point pointexportall_Callback Export all point data ind pointfind silent Find neareast point 152 15 6 SEGMENTATION SUPERUNIT pointforward_Callback Track point forward in time pointmaketimeresolvedthis_Callback Converts a none time resolved point to a time resolved point pointmove_Callback dx dy Helper function to move points pointrenametemplate_Callback Rename points according to a renaming template pointrenamethis_Callback Rename point 15 6 3 LV segmentation unit The purpose of the LV segmentation unit is to provide tools for automated and semi automated segmentation of the left ventricle from either Cardiac MR Cardiac CT or Myocardial Perfu
156. pex of the heart pmin pmax findavpoints x y Rewritten by Einar Heiberg insired by old code by Helen Soneson Find max curvature max curvature is at AV plane ind findcine no Helper function to find corresponding cine image minrange maxrange findrange colorval Helper function to find the range for colordata uses checkboxes also in GUI x y getanatomicalcontour frame Converts the strain contour to an anatomical contour so that it can be plotted on the anatomical image This code is heavily inspired by importsegmentation in segment_main outframe getanatomicalframe frame Returns timeframe in anatomical image that corresponds to frame frame is typical current time frame of strain image xofs yofs fx fy getconversionfactors Get conversion factors between strain coordinate system and anatomical system colorval getparameterdata Returns the parameter data that should be plotted l getpointspos n Distribute the points evenly 217 CHAPTER 15 UNIT IMPLEMENTATION radstrain longstrain totstrain getsectors strainno Get strain in 17 sector format graph Callback plots strain over time from one long axis projection importfromcine_Callback Written by Einar Heiberg Import segmentation from SSFP image initgui no Initiates and open the strain GUI initialize no This function initializes the mesh using data from SET no EndoX pp ee tt initializemesh x y Initializ
157. pporting mat files and 32 auxillary files In addition there are 12 000 lines in around 40 files and 300 subfunctions of internally support lines of code keeping track on distribution compilation process packaging documentation generation etc This Technical Manual aims to describe how to write own plug ins that inter face with the software and give some implementation details for the interested reader A good technical overview of the Segment project is also given in 1 Before reading this user manual the reader should be well acquainted with Segment and programming in Matlab This manual is not a manual how to use Segment it s intention is only to give technical details on how things are implemented in Segment Some implementational details are also given in the user manual 23 10 Architectural Design The entire Segment block can be divided into ten function superunits Some of these function superunits are coded in a single m file whereas some can be further divided into function units and separate m files An overview on how they communicate and relate to each other is shown in Figure Overviews of the Report and File superunits are shown in Figure 5 and Figure 6 respectively Resources Segmentation gt Unit calls unit Called from GUI Figure 1 Overview of the function superunits which constitute the main building blocks of Segment and transaction analysis 25 CHAPTER 10
158. r Size of Dxx is nnodes x nnodes P setupnewboundaryfunctionsglobal no This is the basis function used in the strain paper 2012 08 14 H setuptemporaloperator no H is dtt operator The size is nframes 1 x nframes 1 sigmaedit_Callback Edit box for sigma 220 15 10 ANALYSIS SUPERUNIT sigmaslider_Callback Callback for the sigma slider xnew ynew strain2anatomicalcoords x y Converts from coordinates in strain coordinate system to anatomical coordinate system Srad Slong Sshear Stot straintensor no dx dy Calculates and decomposes the strain tensor to radial long and shear strain timeslider_Callback Called when user changes timeslider trackandcalculateglobal no Perform tracking and calculate strain trackandcalculateglobaleval no Track without using user interface trackmanualandcalculate Recalculates the mesh taking corrections into account translatecontour_Callback direction Callback to translate anatomical contour translatestraincontour_Callback direction Translate the strain contour callback translatestraincontourhelper no dx dy Helper function to translate strain contour undomanualcorrections_Callback Undo manual corrections Currently not implemented returns messagebox viewlistbox_Callback Called when user clicks in view listbox Currently not fully implemented and not called viewlocal Visualize the local basis regionality 221 CHAPTER 15 UNIT IMPLEMEN
159. rawstack object If all return values are the same return true If not return false cropbox fixcropbox self cropbox If cropbox is invalid or empty return a cropbox that doesn t crop anything vencskip fixphases self Make sure phases are numbered from 1 to numphases That is remove holes from the phase numbering r getaccessionnumber self Returns acessionnumber Takes the accession number from the first image r getacquisitiontime self Return the first lowest aquisitiontime found in the dicom files r getbitsstored self Return BitsStored if all dicoms agree else throw error dimsizes getdimensionsizes self cropbox Gets the size of each dimension i e number of frames depth x size y size r getechotime self EH If different values then return a vector This is necessary since a timeresolved image stack may have different echo times This feature is used for T2 T2 mapping See the function t2star m for more details r getflipangle self Return flipangle if all dicom files agree else return 0 r getifcommon self method Calls method for all dicom files in the rawstack object If all return values are the same return that If not throw error 191 CHAPTER 15 UNIT IMPLEMENTATION r getimagetype self Returns image type if all dicoms agree else return Mixed Image Types r getmodality self Return modality if all dicoms agree else throw error r getnumbe
160. rent tasks This boolean coding convention is histor ically not followed but should be followed for new code and old code should sucessively be rewritten Temporarily variables should be avoided and if they are used they should not have a scope that exceeds three lines of code Also here this is something that historically is not always followed This rule should be followed for new code and old code should sucessively be rewritten 6 7 Units The units of variables should be in SI units and the exact unit should also be documented in a comment on the same line as where the variable is ini tialized or calculated For instance speed length time m s 6 8 Graphical user interfaces All new graphical user interfaces should be based on the class mygui When doing so Segment automatically will remember the position of the user inter face and coding is considerably simplified so that one does not need to use 15 CHAPTER 6 CODING CONVENTIONS persistent variables to get application data Please consult the documenta tion of mygui for further details Graphical user interfaces that do not use mygui should be rewritten to use mygui 6 9 Indentation and spacing Matlab standard indentation system is to be used but with using the tab size to two spaces instead of the default four Spacing and use of parenthesis is to be used to enhance readability For instance e A 12 instead of A 12 e if a gt b d lt e instead o
161. ricle in magnetic resonance imaging BioMed Research International In press 2015 H Soneson J F Ubachs M Ugander H Arheden and E Heiberg An Improved Method for Automatic Segmentation of the Left Ventricle in Myocardial Perfusion SPECT J Nucl Med 50 2 205 13 2009 H Soneson F Hedeer C Arevalo M Carlsson H Engblom J F Ubachs H Arheden and E Heiberg Development and validation of a new automatic algorithm for quantification of left ventricular volumes and function in gated myocardial perfusion SPECT using cardiac mag netic resonance as reference standard J Nucl Cardiol 18 5 874 85 2011 E Heiberg H Engblom J Engvall E Hedstrom M Ugander and H Arheden Semi automatic quantification of myocardial infarction from delayed contrast enhanced magnetic resonance imaging Scand Cardiovasc J 39 5 267 75 2005 E Heiberg M Ugander H Engblom M Gotberg G K Olivecrona D Erlinge and H Arheden Automated quantification of myocardial infarction from MR images by accounting for partial volume effects animal phantom and human study Radiology 246 2 581 8 2008 E Heiberg H Engblom M Ugander and H Arheden Automated Calculation of Infarct Transmurality In JEEE Computers in Cardiology pages 165 168 Durham USA 2007
162. ring to make macro evaluation possible 15 4 18 mygetframe m Same as getframe but with error checking for multiple screens Also makes sure that the frame is visible on screen Einar Heiberg 15 4 19 mygetlistbox m Get value from a listbox handle Used instead of normal get to also be able to use macros in Segment 15 4 20 mygetnumber m Input dialog function that get a scalar value Syntax MYGETNUMBER STRI DEFAULT MIN MAX Where PROMPTSTRI prompt for dialog TITLESTRI title of dialog box DEFAULT is default value 117 CHAPTER 15 UNIT IMPLEMENTATION lt MIN gt optional minimal value lt MAX gt optional maximal value 15 4 21 mygetslider m Get value from a slider handle Used instead of normal get to also be able to use macros in Segment 15 4 22 mygetvalue m Get value from a slider handle Used instead of normal get to also be able to use macros in Segment 15 4 23 mygui m MYGUI Class for handeling GUI s in a efficeint manner G MYGUI FIGFILENAME lt BLOCKING gt The purpose of this class is to facilitate to generate GUI s than can also work as a temporary containter data for that so that data transfer between subfunctions becomes simple If blocking is specified then segment internal blocking figure mechanism will be used The function also keeps track of position for the gui to be saved later and to be able to set position of messageboxes called with for
163. rloaded in CVQgui RVQgui and Segment CMR GUI If making major changes make sure to update csegment updateicons JU updateprefhandles g Updates PrefHandles Called by segpref update Overloaded in CVQgui and RVQgui Default folder locations updateprefhandlesadvanced g Called by segpref updateadvanced Overloaded in SegmentGUI and RVQGUI updatetimethings g no mode This fcn is called from switchimagestack and disables enables features that are not available depending of the image stack is timeresolved or not Overloaded in CVQgui updatetitle g Updates titleline of main GUI Overloaded in CVQgui updatevolumeaxes g Called by segment_main updatevolume versionhello Versionhello overloaded in CVQgui RVQ SegmentTransfer Functions in segmentgui m checkversion g Check if new version is available 97 CHAPTER 15 UNIT IMPLEMENTATION copyrvendoforward Overloads empty method in maingui failedaborted g Message when a function is aborted initmaintoolbar g Intialization of main toolbar If new handles are added add those to list in killhandles m as well licensemsg m Display license message g segmentgui programversion Constructor tip singleframetip Return tip for single frame mode switchtoimagestack_part2 g no switchtoimagestack continued Overloads method in maingui updateicons g mode Update icons when new mode is selected Overloads main GUI
164. rofaverages self Return number of averages if all dicom files agree else return 1 r getpatientinfo self Return patient info struct if all dicoms agree If they don t agree try setting all heartrates to zero and return if they agree If that didn t work either throw error r getrepetitiontime self Return the repetitiontime if all dicom files agree else return 0 r getresolutionx self Return resolutionx if all images agree else throw error r getresolutiony self Return resolutiony if all images agree else throw error r getscanner self Return scanner if all dicom files agree else throw error r getsequencename self Returns sequence name if all dicom files agree else return Mixed Sequence Names r getseriesdescription self Return series description if all dicom files agree else return Mixed Series Description r getseriesnumber self Return series number if all dicom files agree else return 0 192 15 9 FILE SUPERUNIT r getslicethickness self Return slicthickness if all dicom files agree else return 1 r getspectspecialtag self Return spect special tag if all dicoms agree else throw error r getstudyid self Returns StudyID Takes StudyID from first image Should be same for all images in the entire study r getstudyuid self Return study uid if all dicoms agree eles throw error r gettimeincr self nFrames Calculates the timeincrement If there is
165. romcontour X Y nbr_points select points from X Y with probability higher when derivative magnitude in respect to distance to mass centre is large previousallframe_Callback Displays previous time frame in current image panel For all other visible image stacks they are adjusted to show correspondig part of the cardiac cycle previousframe_Callback Displays previous time frame of current panel putpin_Buttondown panel type Button down function for pins putpin_Callback panel type Callback to put pins recursekeypressfcn h fcn Helper function to create callbacks to keypressed function z remap im cmap c b Remap data according to cmap renderstacksfromdicom no Render image stacks in main gui This function is typically called upon loading resetguipositions Resets GUI positions of Segment 85 CHAPTER 15 UNIT IMPLEMENTATION resetlight_Callback Activated by toolbar icon different from contrast_Callback below resetpreview Reset preview structure in DATA Preview z reshape2layout im no panel outsideelement Convert a 3D array to an layout ed image with cols and rows rotatetemp alpha This function should late be replaced with qa tool that rotates objects just as scale and move does saveguipositiontodisk Save guipositions to disk scale_Buttondown type panel Button down function for scaling of objects contours scale_Buttonup type Button up function for scaling scale _Motion rese
166. rs but not general segmentation module or time resolved annotation points seted_Callback Set diastole to be current timeframe setes_Callback Set systole to be current timeframe setheartrate_Callback Set heart rate of current image stack setimagedescription_Callback Set the image type image view plane and imaging technique for current image stack 176 15 8 TOOLS SUPERUNIT setimageinfo_Callback Asks for and sets image details of current image stack slidingaverage_Callback Performs sliding average of an image temporalmeanvalue_Callback silent Calculate temporal mean image by averaging over time translatecontour_helper dx dy translateimage Helper function to translate contours and image If translateimage is true then image is also translated Not yet supported Scar MaR Pins Levelset translatecontours dx dy Translate all contours Called by hotkeys x translatecontours_helper x Fix out of bounds indices translatecontoursandimage dx dy Translate all contours and the image Called by hotkeys undosegmentation_Callback no Revert segmentation from undo history upsampleimage_Callback f Upsamples current image stack in slice only Takes care of segmentation in the upsampling process newvol upsampleslices f vol silent Upsamples along last dimension Limitation input must be single or double upsampleslices_Callback f Upsample current image stack in slice direction
167. rt Export data to clipboard figurel_KeyPressFcn hObject eventdata Keypress functions for GUI 211 CHAPTER 15 UNIT IMPLEMENTATION generatepushbutton_Callback Callback to generate new aligned perfusion image stacks containing timeframes between user defined start and end points stricell getahastring Return cell containing strings of segment names from AHA 17 segment model result getbloodpoolcurve no Calculate signal intensity curve of bloodpool endox endoy epix epiy getroisegmentation no Get myocardium segmentation from ROI generated by contraction function init Initiate GUI initimageaxis field Initiate image axis with images from current stack maxslope initplot field ahamat Initiate plots of curves roth initrotatehandle h field midpoint Draw handle used for rotation of image initsliceslider zsz Initiate slider for toggling between slices in display inittimebar field analysed Initiate timebar axis for image specified by input parameter field nextpushbutton Callback field Callback for next frame pushbutton for image specified by input parameter field playalltogglebutton_Callback hObject Callback for toggle button playing rest and stress image stacks in a synchronized manner where they reach their end timeframes simultaneously playtogglebutton_Callback hObject field Callback for play togglebutton for image specified by input parameter field 21
168. rting of the studies ExportList contains a list of studies to be exported to PACS Hostname contains hostname for exporting studies Port contains port for exporting studies Called_AE contains Called_AE for exporting studies StoreSCU contains the StoreSCU for exporting studies folder2load contains the folder to load data from used in importing studies from disc or CD DateNum contains a timestamp when the database was last loaded from disc The datastructure for the patient database is as follows 198 PathName a full path to where the study is stored IsDicom binary variable true if the study is in DICOM format Name a string containing the name of the subject ID a string containing the ID of the subject Sex a string containing the sex of the subject May also be empty if not known 15 9 FILE SUPERUNIT e StudyDate a string containing the study date as reported in the DI COM files or in the mat file e ReceivedDateNum the time when the study was imported or stored in the database in numeric format same format as the now command e ReceivedDateString the time when the study was imported or stored in the database in plain text format e Modality as recorded in the DICOM or in the mat file e FileFormat is either Dicom or Segment e CommentPath reserved for future use currently empty e Mem contains the amount of memory the study takes on disk in bytes If the database needs to be moved all the refer
169. s in the Reference Manual First frame played in a movie Initiated by SET NO CurrentTimeFrame but needed for cal culation what frame to display when playing a movie See also DATA StartTime Seg intersection Intersection image ShowIntersectionMaShow intersection mask BalloonLevel BALLOON EndoBalloonForce EpiBalloonForce LevelSet DATASETPREVIEW 40 Used to determine if the field DATA BALLOON needs to be recalculated Stores the parameter that was used last time to calculate DATA BALLOON A matrix of the same size as SET NO IM contain ing the radial balloon force For further details see 2 3 Used in the automatic LV segmentation for MR images Used in the automatic LV segmentation for MR images Helper structure to SET NO LevelSet DATA LevelSet stores parameters that are pertinent to the graphical user interface that does not need to be stored in SET NO LevelSet A 64 x 64 N array containing the preview thumb nails where N is the number of image stacks EndoEDGEO ENDOEDGE1 ENDOEDGE2 ENDOEDGES3 EpiEDGEO EpiEDGE1 EpiEDGE2 EpiEDGE3 EndoEdgeDetected EpiEdgeDetected MovieFrame NumPoints Edge image of the endocardium in the first direc tion For further details see 2 3 See above See above See above Edge image of the endocardium in the first direc tion For further details see 2 3 See above See above See above True if the edg
170. s in curdicoms type r render self datapath cropbox Renders the images in the loader object to a Preview or a set struct suitable for passing on to segment m im desc filetype resolutionx resolutiony cancrop renderpreview self Renders a preview of the files in the loader object r renderrotstacks self datapath cropbox lines imaxis This rendering method is used when the files loaded are dicom files It s called from the render method r renderstacks self datapath cropbox This rendering method is used when the files loaded are dicom files It s called from the render method 184 15 9 FILE SUPERUNIT s second tfrac Convert from tfrac to minutes self segloader Constuctor Initiate all properties setpreviewmode self Set preview mode to on r uniquelines self Get all the unique lines from the dicom files in the loader object A line consist of the orientation vectors vector parallel to the x and y axis of the picture and a projection of the imageposition onto the subspaces that the orientation vectors span We need this projection to separate projection to separate stacks with the same orientation but diffrent positions r uniquenormals self Gets all the unique normal from the dicom files in the loader object Used in isrotaded method Functions in segdicomtags m a addstructs a b Add fields from struct b to struct a implicit checkFunctionalGroup group group
171. s is neccessary since the compiler script excludes are toolboxes but the specifically indicated toolboxes This is done in order to minimize the size of the compiled project Large projects will take long time to start since they need to be virus scanned before starting and the size also affects the real time unpacking To help to locate the required toolboxes use checktoolboxdepency m e M files in the project You need to add normally used m files here It is not enough to only add it to the SVN tree you need to add it to makeit m Failure to add a file to makeit m will most probably not affect the standalone file but it will affect when compiling to a source code format See also under Section Modules below 238 18 4 MULTI PLATFORM SUPPORT Internal M files Here files that are only required for the maintenance of the entire software project are listed The only reason to list them here is so that they will be included in the total project count when counting the total number of files and lines in Segment project Fig files Here you list all required fig files Failure to include a file here will affect both the standalone version as well as the Matlab version Mat files Here you list all required mat files Failure to include a file here will affect both the standalone version as well as the Matlab version Plugins Here you list all plugins that should be available in the stan dalone version You need only to add the main
172. s to be redrawn drawviabilityhelper no panel Function to draw viability contour on screeen used from drawimageslice drawimagemontage showedits no Show edits overlays of scar and mar if current mode showmaredits no Show MaR edits on screen as a temporary overlay showviabilityedits no Show viability edits on screen as a temporary overlay updateannotationpoints no panel Update coordinates of annotation point handles updatecontours no panel Update coordinates of contour handles of one view panels updateglazoomstate no ysz updateinterp no panel Update coordinates of interpolation point handles updateintersectionpoints panel Draw intersection with segmentation in other image stacks 103 CHAPTER 15 UNIT IMPLEMENTATION updatelongaxiscontours arg no panel Update coordinates of contour handles for HLA or VLA image view updatemeasures no panel Update coordinates of measurement handles updatemodeldisplay no panel Update data used to correctly display segmentation in montage view This fcn needs to be called when the segmentation has changed updatemontagecontours no panel Update coordinates of contour handles for montage image view updatemontageinterp no panel Update coordinates of interpolation point handles for montage view updatemontagemeasures no panel Update coordinates of measurement handles for montage view updatemontagepins no panel Update coordinates of pin handles for mont
173. see Section Same as DICOM tag ImagePosition If not pre sented then set to 0 0 0 Contains position in mm in 3D of the upper left pixel in the top slice in the image stack For further details on coordinate sys tems see Section ImageType Type of images that the image stack depicts The field is used when identifying what image stacks to use for different analysis If not set at loading then Segmenttries to figure these details out by looking at what operations have been performed on what image stacks Currently applied values are e General Generic Image type if not spec ified identified e Perfusion Rest e Perfusion Stress e Strain FFE Strain Fast Field Echo e Strain TFE Strain Turbo Field Echo e Late enhancement Viability e Cine e Scout e Qflow e T2Stir e T1BB 93 CHAPTER 13 SET VARIABLE 54 ImageViewPlane View plane of images that the image stack de picts The field is used when identifying what im age stacks to use for different analysis If not set at loading then Segmenttries to figure these details out by looking at what operations have been per formed on what image stacks Currently applied values are e Unspecified Generic Image view plane if not specified identified 2CH Long axis 2 chamber view gt 3CH Long axis 3 chamber view 4CH Long axis 4 chamber view Sagittal Coronal Fr
174. segmentation data so undo i possible This should allways be called before routines that change the segmentation enddiastole_Callback noupdate change current time frame to end diastole enddiastoleall_Callback Change current timeframe of all image stacks to end diastole endsystole_Callback noupdate Change current time frame to end systole endsystoleall_Callback Change current timeframe of all image stacks to end systole extraslice_Callback type Add an extra slice Type is either basal or apical Takes also care of delineations flip_Callback dim Helper function to image stack flipping tools flipt_Callback Helper function to flip in t direction Takes care of segmentation a b flipvars b a Flip variables Simple and elegant flipx_Callback Flip x direction of current image stack Need to flip both x and z to maintain a righthand system 173 CHAPTER 15 UNIT IMPLEMENTATION flipx_helper Helper function to flip in x direction Takes care of segmentation flipxy _helper Interchange z and t of current image stack Takes care of segmentation flipxz_Callback Interchange z and x of current image stack Takes care of segmentation flipy_Callback Flip y directon of current image stack Need to flip both y and z to maintain a righthand system flipy_helper Helper function to flip in y direction Takes care of segmentation flipz_Callback Flip z direction of current image stack Nee
175. sion SPECT MPS The used seg menation algorithm for CMR is described in 8 The used segmentation algorithm for MPS is decribed in 9 and 10 Interactions This unit calls the Helper functions superunit to handle mouse input from the user and the Draw superunit to make graphical updates It is related to the Contours unit described in Section 15 6 5 that are used to copy and import segmentations between image stacks The RV segmentation unit described in Section shares code with the LV segmentation unit Datastructure The LV segmentation is stored in the SET variable and specifically the fields EndoX and EndoY The units are pixels Functions The functions for lv segmentation in CMR images are described in the file lv m The functions for lv segmentation in CT images are described in 153 CHAPTER 15 UNIT IMPLEMENTATION the file CTLVSegmentation m The functions for lv segmentation in MPS images are described in the file spectlvsegmentation m These files are not autodocumented in this Technical manual since it contains propriety algorithms Please consult the lv m and spectlvsegmentation m files for details instead 15 6 4 RV segmentation unit The purpose of the RV segmentation unit is to provide tools for semi automated segmentation of the right ventricle The used segmenation algorithm is a quick modification of the LV segmentation algorithm s The code is imple mented in the file rv m but does also share code wit
176. st argument is not supplied the choice of naming the roi to ROI n is disabled name roiasktemplate no function used for asking for name of roi template roiclearall_Callback clear all ROIs roicopyalltimeframes_Callback n copy ROI to all time frames 164 15 6 SEGMENTATION SUPERUNIT roicopydownwards_Callback n copy ROI one slice downward roicopyendo_Callback Copy from endocardium to a ROI roicopyepi_Callback Copy from epicardium to a ROI roicopyfromotherimagestack_Callback Copy roi from other image stack Let user select from which image in an input dialog roicopymar_Callback Copy from scar to a ROI roicopyscar_Callback Copy from scar to a ROI roicopyupwards_Callback n copy ROI one slice upward roidelete_Callback n delete ROI n roiexportvalues_Callback Get what ROI s to take no roifindmag no Find magnitude no roiforce_Callback Function to set force shape over time in menu checked and unchecked roiforceapply function to force shape over time m roiget stri arg Gets roi either by getting closest ROI to clicked coordinates if two input arguments or by selecting in a pick list 165 CHAPTER 15 UNIT IMPLEMENTATION roisign roiguessign nom nop currentroi Guesses sign of the roi to make the net flow through the roi be positive roihistogram_Callback Make intensity histogram from ROI with either normalized intensities or true intensities Uses roiselector to
177. sure in mm Name String containing the name of the measure Functions measure _Buttondown panel Button down function for measurements measure Motion ind Motion function for measurements measureexport_Callback Export measurements measuremove_Callback dx dy Helper function to move measurements measurepoint_Buttondown panel Buttondown function fore a measure ment point marker measureput Buttondown Called when a measurement point except the endpoint is placed measure Buttonup Button up function for measurements stri lstr measureasklabel g Asks for a label of a measurement measureclearall_Callback g Clear all measurements measureclearthis Callback g Clear current measurement measurefontsize g panel index Sets measure font size measurerenamethis_Callback g Rename current measurement 15 6 2 Annotation point unit The purpose of the Annotation point unit is to allow the user to place anno tation points in an image Interactions This unit calls the Helper functions superunit to handle mouse input from the user and the Draw superunit to make graphical updates Datastructure The SET struct has a field Point which is a Struct that contains position of annotation points The struct has the following fields e X 1x N vector with X coordinates where N is the number of annota tion points 151 CHAPTER 15 UNIT IMPLEMENTATION e Y 1x N vector with Y coordinates e T 1x N vector with time frames i e one f
178. t Motion function for scaling selectallslices_Callback Selects all slices in current image stack setcurrenttimeframe frame function to set current time frame input argument is frame to be set to current time frame slowerframerate_Callback Makes movie play slower stopmovie_Callback End movie display switchtolongaxisslice slice laxfield silent Called when slice has changed in HLA or VLA view 86 15 1 MAIN SEGMENT SUPERUNIT switchtopanel panel updateimagestack Make panel the currentpanel switchtoslice slice Called when current slice has changed If slice has changed make sure montage one are in sync Does nothing if slice CurrentSlice systolelistbox_Callback function called when changing longaxis motion in list box thumbnail_Buttondown Buttondown fcn for thumbnails thumbnail_Buttonup Buttonup fcn for thumbnails thumbnail_Motion Motion fcn for thumbnails out thumbnailno in Helper fcn to remember what image stack were clicked thumbnailslider_Callback varargin Slider callback for thumbnail slider timebar_Buttondown Button down function for the time bar in the volume graph timebar_Motion Update current timeframe when user clicked in volume graph unlighttool h Helper function to change color of a tool to represent unselected unselectallslices_Callback Unselects slices in current image stack update_thumbnail nos This fcn updates thumbnail no 87 CHAPTER 15 UNIT
179. tation viabilitymenu no Update the viability menu helper function viabilitymode_Callback mode Select different modes for viability and updates the menu accordingly gt weighted Radiology paper method fwhm full widht half maximum gt sdfromremote sd from remote otsu treshold method based on otsu s threshold em threshold method based on the Expectation Maximization EM algorithm Imp 160 15 6 SEGMENTATION SUPERUNIT viabilitynoreflow_Callback Toggle setting viabilityreset_Callback mode no Callback to reset all scar settings viabilitysetbeta_Callback Set the curvature beta used in the levelset part of the viability algorithm s viabilitysetminvolume_Callback Sets minimal volume for a single infarct viabilitysetsdfromremote_Callback Set number of standard deviations from remote viabilityshowgrayzone_Callback Show overlays of core dark red and greyzone dark yellow viabilityshowinfarctaswhite_Callback show Show infart as white overlay viabilitytoggleweighted Toogle to weigted mode viabilitytoggleweighted_Callback Toggle usage of weighted method viabilityupdatedirect_Callback Callback to toggle direct update of viability Only reason for not haveing direct update is large exvivo data sets where it takes lots of time to recalculate after changes intweight varargout viabilityweight no Finds intensity mapping of infarct for weighted algorithm 15 6 7 Myo
180. tent boldcells width TABLE Method to insert a table with content specified by a cell stri text hg paragraph alignment TEXT Method to write a paragraph of text 145 CHAPTER 15 UNIT IMPLEMENTATION write hg str Writes a string of characters to file columns fg varargin COLUMNS Method for dividing input into columns call conc varargin Concatenate two or more function calls fg figgenerator title pathname filename pagewidth lineht Constructor gsstri ftext fg FTEXT Method to write a paragraph of text with formatted headlines call headline fg headtext lpos HEADLINE Method to write a headline in bold hline fg HLINE Method to write a horizontal line call image fg imgname imgsource lpos IMAGE Method to add an image imgsource can be a location or an image matrix call newline fg NEWLINE Method to insert a line break newpagepos pagebreakchk fg pagepos nextblock PAGEBREAKCHK Method to insert a page break Checks if it is time to insert a page break using pagepos parameter start fg figtitle START Method to open a new figure stop fg STOP Save all figures to image files then close them call table fg content boldcells width lpos TABLE Method to insert a table with content specified by a cell call text fg paragraph alignment lpos weight TEXT Method to write a paragraph of text zoom fg ZOOM Zoom to current page size 146 15 5 REP
181. ting in the prefer ences In the future I plan to also include the modified center line method Note that the centers are calculated for each timeframe separately Wall thickening is defined as the wall thickness in end systole minus the wall thickness in end diastole Note that it is possible to manually or automati cally select what timeframes that are diastole or systole respectively Fractional wall thickening is defined as 5 Where WT is fractional wall thickness and WT is wall thickness and WTgp is wall thickness in end diastole In the bulls eye plot then fractional wall thickening is showed in end systole 70 14 9 CALCULATION OF REGURGITANT VOLUMES AND SHUNTS 14 9 Calculation of regurgitant volumes and shunts The regurgitant fraction for the aortic valve and the pulmonary values are calculated as pan E 6 U forward where r is regurgitant fraction Vback is backward volume and Uforwa is for ward volumes Backward volumes is taken as timeframes where the net flow is negative and integrated over the entire cardiac cycle The regurgitant fraction for the tricuspid and mitral valve are calculated as SV Uforwd 100 7 E SV 7 where r is regurgitant fraction and SV is stroke volume for left or right ventricle respectively Uforwa is forward volume The Q Q ratio is defined as Qp Q where 2 is the stroke volume of the pulmonary artery and Q is the stroke volume of the aortic artery
182. tion of the heart and its major vessels using multi slice multi frame and velocity encoded MR images It provides clinically relevant and reproducible data for supporting the evaluation of the function of the chambers of the heart such as left and right ventricular volumes ejection fractions stroke volumes peak ejection and filling rates myocardial mass regional wall thickness fractional thickening and wall motion It also pro vides quantitative data on blood flow and velocity in the arterial vessels and at the heart valves Segment is tested on MR images acquired from both 1 5 T and 3 0 T MR scanners The data produced by Segment is intended to be used to support qualified cardiologist radiologist or other licensed profes sional healthcare practitioners for clinical decision making It is a support tool that provides relevant clinical data as a resource to the clin CHAPTER 1 REGULATORY STATUS ician and is not intended to be a source of medical advice or to determine or recommend a course of action or treatment for a pa tient 1 3 Investigational purposes None of the organizations persons named in conjunction with the software can accept any product or other liability in connection with the use of this software for investigational purposes 2 License terms For general license terms of the usage of the software see the User Manual Though parts of Segment is be released in source code form this does not imply that standard
183. tions helpimageposneg im sector konst Helper function to display image 15 5 4 Flow unit The purpose of the Flow unit is to quantify and report flow data from phase contrast images Interactions This unit interacts with the Calculation superunit for assistance in some calculations The Export unit is called for export of data Datastructure The data used for flow analysis is contained in the Flow field of the SET struct Functions expandflowroi no m d Expand the roi M outwards by D mm s flow3dmovie_Callback arg scaling no up down left right Displays 3D movie of velocity in a vessel flowcreate_helper angio Helper function to create flow derived image stacks 127 CHAPTER 15 UNIT IMPLEMENTATION flowcreateangio_Callback Create angio image flowcreatevelmag_Callback Create velocity magnitude image flowdelete_helper angio Helper function to delete angio images flowdeleteangio_Callback Delete angio image flowdeletevelmag_ Callback Delete velocity magnitude image floweddycurrent_Callback arg Callback for menu selection to do eddy current compensation ok pulmno pulmroi aortno aortroi flowfindqpqs Find data sets with pulmonary and aortic flow to use for Qp Qs analysis flowfix n temp function to flip 2d flow directions flowflipdirs_Callback Flips LR and UP direction flowflipleftright_Callback Flips up down direction flowflipupdown_Callback Flips up down direction
184. titution applylight_Callback 171 CHAPTER 15 UNIT IMPLEMENTATION Apply current light setting to current image stack Makes permanent changes in the IM field autoesed_Callback silent no Autodetect and store ED and ES closesetimagedescription_Callback Close the gui for setting the image description copydownward_Callback type silent dolv lvalg Copy segmentation in current slice downwards and refine copyforwardselected_Callback lv Copy segmentation of selected slices forward in time copyupward_Callback type silent dolv lvalg Copies upward and refine type is either endo or epi silent is true if to avoid graphic update if dolv false then copy rv crop_Buttondown panel Buttondown function to crop the image stack crop_Buttonup Buttonup function for cropping of image stacks crop_Motion Motion function to crop the image stack outx outy cropcontour inx iny isroi Used to crop and reinterpolate contours nos crophelper no0 xind yind This function is the enginge in cropping cropspecial undocumented function cropupdate nos Update image after a crop 172 15 8 TOOLS SUPERUNIT disableundo no Disable undo function Also copies segmentation data to make sure data is consistent duplicateimagestack_Callback Duplicates current image stack This function breaks links to linked datasets parent and children enableundo no Enables undo function in menus and icons Also copies old
185. to default values Called by segpref default Callback Overloaded in CVQgui RVQgui Segment CMRgui dispwelcometext g Displays welcome text Overloaded in CVQgui SegmentCMR GUI drawroiinpanel g panel Draw ROI s in one slice mode drawsectorgrid g no Overloaded in RVQ GUI drawvolume g Draw volume curve Overloaded in CVQgui enableopenfile g Called by openfile enablesegmentgui Overloaded in CVQgui and RVQgui filecloseall_Callback g silent Deletes all image stacks and resets Segment to original state Overloaded in CVQgui and RVQgui fileopen_Callback g Loads a set of files as a 4D volume and also updates preferences Calls the fcn openfile which displays the fileloader GUI Overloaded in CVQgui fail filesaveallas_Callback g pathname filename Overloaded in some other GUI s filename generatesavefilename Called by segment filesaveallas_Callback Overloaded in CVQgui pathname getpreferencespath g Get path to preferences folder value getthisframeonly g Function to check thisframe onlye mode or not 92 15 1 MAIN SEGMENT SUPERUNIT heartratezero g heartrateest React upon a heart rate read as zero from DICOM in openfile initset iconcallbackhelper handle callback Helper function to updateicons handle iconcdatahelper handle icondata tiptext Helper function to updateicons type viewplane technique imagedescription Define the image types ima
186. troduction Compiling Segment is a complex process since there are many depending files that need to be included Therefore a make script makeit m was created This script contains a list of all files required in the entire Segment project With the addition of new Segment products the script was refactored into an object oriented approach using a hierarchy of compilation script classes This class hierarchy is described in Chapter 11 When making new files it is therefore necessary to include the new files in the compilation class definition files for softwares in which the file is to be used Compilation is in this chapter used in its widest sense including not only making a executable standalone application but also the creation of a zip file for distributing Segment in a source code format or generating all documentation files A major part of the script is the control of which files should be included and to ensure that the files are properly protected when distributing as a source code format 18 2 Running the compilation script The first thing one need to do before compiling Segment is to update the file changelog m with the current version number i e release number This information is used when creating the output file The script can run in four modes and upon running internaltools makeit ma GUI prompts the user to select one e Make Segment standalone make a standalone research edition exe cutable suitable for installat
187. udio 2010 Pro fessional This version is bought by Medviso and disc are availble in main office 240 18 6 SECTRA PLUGIN COMPILATION To download the environment click in CSN in Sectra web see details in wiki SectraPlugin for log in details Click on Download CAI SDK and take the latest release You start Microsoft Visual Studio by clicking on sectraplugin sln To compile click on Build Build solution In the box select Release and not Debug Select platform Win32 or Win64 The the compilation is finished then the sectraplugin dll is found in the Release folder If you compiled 64 bit version then it is found in the x64 Release folder Check in the version in the system as either sectraplugin32 d11 or sectraplugin64 d11 241 19 How to Create Own Plug ins The easiest method of how to learn to make own plug ins is to study the example plugin template m Writing own plug ins is a great way of spread ing your algorithms to users all over the world and also to contribute to the Segment project For more details on how to contribute or learn more about interacting with other users please see Chapter 20 A plugin file must have a name beginning with plugin m Note that the plugin may of course call other functions that can reside anywhere on the Matlab path When Segment is started the current folder is scanned for functions with this pattern Matching functions are called with the argument getname and a string with the na
188. ultiplanar reconstructions of image stacks 224 15 10 ANALYSIS SUPERUNIT Interactions Interactions are negligible Datastructure The image information on which to operate is taken from the SET struct and the stack number is taken from NO variable Functions buttonup Called upon release of mouse button after center point has been pressed down center_buttondown Called when center point is pressed down sets motion and buttonup function center_motion Called upon mouse motion after center point has been pressed down done Resample the complete volume init Initiate GUI newcut Callback for making a new cut p1_buttondown Called when point p1 is pressed down sets motion and buttonup function p1_motion Called upon mouse motion after point pi has been pressed down p2_buttondown Called when point p1 is pressed down sets motion and buttonup function 225 CHAPTER 15 UNIT IMPLEMENTATION p2_motion Called upon mouse motion after point p2 has been pressed down play Called when start play prevcut Callback for changing to previous cut z resample_cut Do the resampling based on cut selected by user z resample_slice Calculates the slice i e left image panel z impos resampler im region sz no Calculate new image coordinates for resampled image reset_line dummy Line reset callback resolutionedit Callback for when resolution is changed by user sliceslider Callba
189. umber of the dicom line getline self Gets the line of the image A line consist of the orientation vectors and the projection of the position onto the orientation vectors 186 15 9 FILE SUPERUNIT r getmodality self Returns the Modality normal getnormal self Returns the normal to the picture that i the cross product of the orientation vectors r getnumberofaverages self Returns the NumberOfAverages field orientation getorientation self Get the orinentation vectors as a 2x3 matrix r getpatientinfo self Returns a Patientinfo struct with fields gt PatientName gt PatientID gt PatientBirthDate gt PatientSex PatientAge gt HeartRate gt AcquisitionDate gt PatientWeight r getphotometricinterpretation self Returns the photometric interpretation pixelData getpixeldata self Parses and returns the PixelData field pos getposition self Returns the image position in 1x3 vector r getrepetitiontime self Returns the RepetitionTime r getresolutionx self Returns the resolution in the x direction r getresolutiony self Returns the resolution in the y direction 187 CHAPTER 15 UNIT IMPLEMENTATION scanner getscanner self Return the scanner based on the Manufacturer tag r getsegmentdata self Parses and returns the SegmentData r getsequencename self Returns the Sequence Name r getseriesdescription self Returns t
190. ument purpose The purpose of this document is three fold 1 Work as a technical documentation of Segment for Medviso AB 2 Work as a technical documentation for researcher who wish to use the plug in functionality of Segment as described in I 3 Work as a implementation documentation of Segment Therefore all details described in this technical manual may not be applicable to all developers since parts of the source code is only accessable by Medviso AB 11 6 Coding Conventions This chapter describes the coding conventions that has been used when cod ing Segment I have really tried to use a consistent naming rules to ensure that variables are given a logical name However there are occasions where historical reasons have lead to exceptions to the rules given below In general Segment originally used the global variable NO indicating the cur rent image stack quite extensively The use of NO is however not encouraged and it is highly recommendable to in the function call indicate the current image stack Work is ongoing to completly remove the global variable NO but it takes time please see wiki and relevant tickets on this matter 6 1 Naming functions Functions are always named in lower case letters only The underscore letter is not used with the exception of e Callbacks are named as functionname_Callback e Functions for mouse motion callbacks are given names ending with Motion e Some functions have helper f
191. unctions that are only called from other functions with the same name These functions are named helper e Functions for mouse button up down callbacks are given names ending with Buttonup or ButtonDown Note that functions should not be ended with an end Matlabsupports both syntaxes This is with the exception with objected oriented program ming see below 6 2 Naming variables The following rules apply e Global variables have all capital letters i e DATA 13 CHAPTER 6 CODING CONVENTIONS 6 3 Field names of structures and structure arrays are given names start ing with a capital letter When two or more words are concatenated then the first letter of the second word also have a capital letter For in stance DATA CurrentTool Abbrevations are also given capital letters For instance SET NO TSize where T stands for time Field names with all capital letters corresponds to matrices For in stance SET NO IM or DATA BALLOON The use of plural s is very limited and only used where there are limited numbers of values the field and it may be necessary to point out that there are more values than just a scalar For instance DATA ViewPanels is just instead of DATA ViewPanel to point out there are or may be more than one view panel Name graphical handles The graphical handles are named with all lower case letters and no underscore letters Generally the names are rather long and exploratory The following genera
192. utational client with the name NAME METHODS DISPLAY Overloads display SEND B FCN CMD ARG Sends a non blocking message FCN is function handle function that is executed upon return of message The function handle is called with 1 Name of slave 2 Received status 0 sucess 3 Received command 4 Received arguments often empty depends on command Note that there is NO buffering of commands so you can not stack multiple commands If you do not give the slave time to read the message before you send another message SET B PROPERTY VALUE Set property values 114 15 4 HELPER FUNCTIONS SUPERUNIT OK PING B TIMEOUT Pings client OK ALIVE B Test if server slave is alive DELETE B Destructor for class Sends kill command to server slave B MYCLIENTSERVER instanciate object STATUS RES lt ARGS gt SENDBLOCK B CMD ARG Sends a blocking message VALUE GET B PROPERTY 15 4 7 mycopyfile m MYCOPYFILE Copies a file from source to dest MYCOPYF ILE SOURCE DEST Should be platform independent and faster than making a system call If really large files are used then do a system call instead Essentially a wrapper to COPYFILE kept for naming consistency See also MYDEL MYMKDIR 15 4 8 mycountunique m MYCOUNTUNIQUE counts the number unique elements in the input vector N MYCOUNTUNIQUE V lt tol gt N is the number of unique elements V is numeric input ve
193. ware MCR enables the ex ecution of Matlab files on computers without an installed version of Matlab Documentation to end user Installation instructions for MCR are included in the installation instructions for Segment Technical docu mentation this section Method to ensure appropriate use MCR will be installed by the administrator trained by Medviso AB The administrator is responsible for the update of MCR when indicated by Medviso AB Method to ensure the OTS software works The verification of the MCR are included in the Installation Process Verification Control the OTS software The MCR is only upgraded when the development enviroment Matlab is upgraded Matlab is only upgraded when it is considered adventageous for the software development and typically it is 2 4 years between upgrades After an upgrade the MCR is reverified The MCR installer is provided at the same server as the software installation files are 10 2 2 SOUP elements The software of unknown provenance SOUP element used by Segment is the DCMTK library which has the following specifications Manufacturer OFFIS Institute for Information Technology Version 3 5 4 Hardware specifications Not specified Software specifications Opearting system Windows 2000 or later both 32 bit and 64 bit are supported Intended use Handling DICOM files for the hospital PACS system Features Tools for recieving DICOM files from the hospital PACS system
194. with changes in user interface wallthickness_Callback Callback from wallthickness analysis checkbox stri box hg text width BOX Method to insert a text box stri columns hg varargin COLUMNS Method to insert a table without borders used for dividing input into columns stri conc varargin Concatenate two or more function calls gsstri ftext hg FTEXT Method to write a paragraph of text with formatted headlines 144 15 5 REPORT SUPERUNIT stri headline hg headtext prio HEADLINE Method to write a headline in bold stri hline hg HLINE Method to write a horizontal line stri html footer hg Return string used as HTML footer stri html header hg Return string used as HTML header hg htmlgenerator title pathname filename pagewidth Constructor stri image hg imgname imgsource IMAGE Method to add an image Also stores it to disk in the same folder as the HTML file imgsource can be a location or an image matrix stri link hg ref text LINK Method to write a link to a file or URL stri newline hg NEWLINE Method to insert a line break newpagepos pagebreakchk hg pagepos nextblock PAGEBREAKCHK Method to insert a page break Checks if it is time to insert a page break using pagepos parameter hg start hg START Method to open the HTML file and write headers hg stop hg STOP Method to write necessary HTML footers and close file stri table hg con
195. x 0 5 y 0 5 x 0 5 y 0 5 x 0 5 y 0 5 1st again 137 CHAPTER 15 UNIT IMPLEMENTATION X Y gettimeframemarkercoords Computes the timeframe marker vertical line in temporal plot coordinates init force Initialize the Flow Unwrap GUI initializeflowdirectionlistbox Initializes the listbox where flow direction can be selected initializegui Performs startup tasks like setting slider limits A full update is also done after this initialization so there is no need to duplicate code in both initializehidejumpsizeselect Hides the jump size selector initializehideunnecessary Hide unnecessary UI elements If there is only one slice hide slice selection If zoom is 0 hide pan sliders initializesliders Initializes the sliders initializetemporalplot Initializes the temporal plot initializevelocityimage Initializes the velocity image jumpsizebuttongroup_Callback src event Jump size selector callback keypress_Callback src event Handles keypress events 138 15 5 REPORT SUPERUNIT Up 30 Slice Down 31 Slice Left 28 Timestep Right 29 Timestep wW 119 Pixel selector up aA 97 Pixel selector left ss 115 Pixel selector down dD 100 Pixel selector right space 32 Play current slice shift Wrap up control Wrap down movecurrentpixel direction Moves the current pixel in requested direction but stops at boundaries panimageslider_Callback Callback for the pan sli
196. zontal slice of the viewed plane if derived longaxis radvel calcradialvelocity no Calculate radial velocity of the endocardium Forward difference is used meanarea area calcroiarea no roino thisframeonly Calculates roi area helper fcn m sd rmin rmax calcroiintensity no roino normalize thisframeonly Calculates intensity within a ROI helper fcn rows cols calcrowscols no z Calculate a good montage setup so maxiumum number of slices can be displayed on the screen varargout calcrvvolume no Calculate RV volume no is the image stack The RV volume calculation does not involve any longaxis compensation 107 CHAPTER 15 UNIT IMPLEMENTATION calcrvvolumepolar no Calculate RV volume when rotated image stacks xout yout calcsegmentationintersections no type viewtype Calculates intersections between segmentation in image stacks no is image stack and type is endo or epi can also be rvendo etc the type is a string that dynamically calls a field of the SET struct ticks calcticks num res Helper fcn to calculate length of ticks in volumegraph z calctruedata im no Calculate true image intensities as before Segment internal normalization Uses IntensityScaling and Intensity0ffset stored in SET structure im is input image and no is image stack where to take the scaling from calcvolume no Calculate volume of segmentation and updates Updates both lv and rv segmentation Calls subfu

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