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Segment - User Manual

1. Patient Data Name BETE A ALF D 197301010001 Birth Date 19730101 Acquisition Date 120061204 Sex M lago 33 years Height 180 cm Weiche 20 kg BSA HeatRate LV Analysis w Volume versus time Parameter Value Reference values LV Mass g 136 _ 109 185 EV Mass index gh Jas 59 92 m End Diastolic Volume ml 151 121 204 End Diastolic Volume index l m 75 66 101 120 End Systolic Volume mi ar 53 78 E End Systolic Volume index mm 23 18 39 Global Stroke Volume mi 104 79 135 E 100 Forward Stroke Volume PC ml 102 3 Cardiac output PC limin 57 gt a Cardiac output index PC Wein 29 Ejection fraction P4 9 57 75 Longaxis motion mm 15 60 Peak Ejection Rate m s 196 LV volume mi Time of Peak Ejection Rate ms 237 f Myocard volume ml Peak Filing Rate mls 290 200 400 600 800 1000 Time of Peak Filling Rate ms 592 Time ms 2CH Longaxis Image 3CH Longaxis Image 4CH Longaxis Image GENERAL IMPRESSION This patient looks normal Date 2011 03 15 Reviewing doctor Dr Gonz lez Figure 68 Example of a report 179 39 Short Commands Hot keys This chapter describes the hot keys that can be used in the program Note that in many places you can also bring up a pop up menu by using the right mouse key to more easily access frequent menu items 39 1 Hot keys D
2. New cut Resamples into parallel slices to the selected line The cuts are also perpendicular to the viewing direction Previous cut Backs up one level in the cut history The current cut is not saved Done Export Exports the resample image stack back to Segment Play Then this toggle button is selected then the image is played as a movie Close Closes the dialog resampler without storing any information Parameter slice determines the slice distance in mm and output determines 135 CHAPTER 30 IMAGE REFORMAT MPR the output resolution in the new short axis plane Segment Reformater HER View history Output Slice thickness mm 5 0 Resolution mm 1 0 New cut Previous cut Done Export Image volume Cut along line in left panel EE Close Figure 47 Image reformater GUI 136 31 T2 T2 Quantification Module The functions described in this chapter is in US only for off label use and for investigational use In magnetic resonance MR imaging T1 T2 and T2 relaxation times rep resent characteristic tissue properties that can be quantified with the help of specific imaging strategies The purpose of the T2 T2 Module is to quan tify T2 and T2 relaxation times in MR imaging Quantification of T2 and T2 values follows the same underlying mathematical principles but differ ent source images are used T2 changes have been shown
3. 26 2 Report per slice 27 LV Sphericity Analysis 28 Export Images and Results 28 1 Export results to clipboard 28 1 1 All stacks with header 28 1 2 Allstacke 2 2 a 4 4 4 we e 28 1 3 This stack with header 28 14 Thisst ckl coso 2 44 28 2 Export volume curve to clipboard 28 3 Export contour to clipboard 28 4 Export volume of contours per slice 28 5 Export Image ardid en a an 28 6 Export screenshot 28 7 Export movies oso lt lt 28 8 Movie Recorder 29 Customizing Segment 29 1 Image description settingsl 29 2 Advanced and DICOM Settings 29 3 PACS Settings 29 4 Technical details 30 Image Reformat MPR 31 T2 T2 Quantification Module 31 1 Module overview 31 2 Implementation 24 2 28 1 2 244 ola Validation sos e a Reo 117 119 121 ee 121 CA A Ge 121 123 125 vil CONTENTS 141 bp ick d amp Rae Be ee ne oe we Se He 141 Soke Sea 141 32 2 1 Manual corrections 1 4 0 a2 52 44 2 bbe ae ae 143 32 3 Automatic quantification of myocardium at risk 144 33 3 1 Define RV center se a na en a oS eN 144 ee eee ee ere ee eee re 145 ee ee ee ee ee ee AAA 146 Ci ba Pe Ae a ee ee 147 32 4 1 Automatic quantification of stress induced ischemia Last tee cele Orth dak GS ee eG 147
4. Figure 43 Preferences GUI There are four panels in total The top most panels sets default folder lo cations for loading and saving respectively It is also possible to indicate which drive path that corresponds to your CD drive Then the left most panel sets preferences for editing and drawing contours the middle panel sets preferences for regional analysis and the right most panel sets system pref erences The button Advanced System and DICOM Settings opens a new interface with settings for base image path for patient database and DICOM com munication parameters The button PACS Settings opens an interface with settings for PACS communication The option amp Add pins when adjusting contour controls weather points should be 129 CHAPTER 29 CUSTOMIZING SEGMENT placed when manually correcting a contour This option should be checked when modifying time resolved images but unchecked otherwise X Black White view plots the endocardium and epicardium with white lines This is useful for making screen captures for illustrations that are not printed in color The edit box Line width for endo epicardium sets line width for the contours This again is useful for making screen captures Default line width is 1 The edit box Distance to contour for adjustment adjust how close to a contour one need to click before this contour is activate When using the interpolate tool
5. Distance measurements this section contains a table that lists all dis tance measurements performed on the current set of image stacks 2CH 3CH 4CH Longaxis Image this section contains a user selection of longaxis images in end diastole Shortaxis Image this section contains a montage view of all shortaxis image slices in end diastole with delineations included 38 1 Configuration This section describes how the Report Module can be configured 176 38 1 CONFIGURATION 38 1 1 Hospital logo This is an image header that is supplied by Medviso AB to each customer separately Place this file in the folder where Segment is installed 38 1 2 Reference values Reference data used in LV and RV analysis can be selected from a listbox If patient age and sex are present in the patient info the listbox will automat ically suggest a suitable set of reference values If reference data is used in the report patient values outside the range specified by the reference data will be marked in red The name of the used reference data set will also be included in the report A directory contains each reference data set as a text file with the following structure Name Maceira Males Age 30 39 Title to display in listbox ImagingType SSFP Describes used imaging type LowerAgeBound 30 UpperAgeBound 39 Sex M should be either M or F LVM 109 185 EDV 121 204 range EDV_BSA 66 101 BSA means nor
6. Q 2 ox YO gt EA December 11 2015 Software platform v2 0 R4790 MEDVISO AB http www medviso com Griffelv gen 3 SE 224 67 Lund Sweden Tel 46 76 183 6442 Contents 1 Regulatory status 1 1 Commercial usage of Segment Indications for usel 2 2 2222 Investigational purposes 2 A 1 2 1 3 License Terms 2 1 2 4 Free or charge for non commercial research METETE 2 3 Commercial research non human images Future modulesl 3 Acknowledgements Rationale for the Software 5 How to Read This Manual Typographie conventions Trademarks sosse ae Hw ae 6 3 Abbreviations 7 System Requirements 7 1 Operating system Hardware requirements 8 6 1 6 2 1 2 Installing and Uninstalling Installation of Standalone version for Windows 8 1 8 1 1 Installing Matlab Compiler Runtime 11 11 11 11 15 15 15 17 17 17 CONTENTS 8 1 2 Installing Segment 17 8 1 3 Create shortcut Va pu a 2 22 02 24 2245 19 8 1 4 Notes for Windows Vista users 19 8 1 5 Network installation of Segment 2 2 19 8 2 Installation for source code version 20 AE PUNE o eane ee a a a ae ee Ne ee d v 20 8 4 Upgrading Segment comme mn 21 8 5 First time running Segmentl o 21 8 5 1 Setting preferences
7. S Shift D Shift 5 Left arrow Right arrow Up arrow Down arrow Shift Arrows Go to end diastole Go to end systole Go to end diastole in all visible image stacks Go to end systole in all visible image stacks Previous time frame Next time frame Next slice in basal direction Previous slice in basal direction Same ass Arrows but applies to all visble image stacks Start to play cine thumbnail Start to play movie Start to play movie of all visible image stacks Refresh screen Hide show all contours and markers Shift mode in panel between montage and one slice Selects all slices Unselect all slices View all image stacks View one image panel View two image panels View two image panels as rows View three image panels View three image panels as rows View three image panels View six image panels View six image panels as rows View nine image panels 181 CHAPTER 39 SHORT COMMANDS HOT KEYS Ctrl 1 One view Ctrl 2 M mode view Ctrl 3 Montage view Ctrl 4 Montage row view Ctrl 5 Montage fit view Ctrl L Perform fully automatic LV segmentation Ctrl M Segment LV endocardium Ctrl Shift M Segment LV epicardium Ctrl Alt M Segment RV endocardium Ctrl R Refine LV endocardium Ctrl Shift R Refine LV epicardium Ctrl Alt R Refine RV endocardium Alt R Refine Flow ROI Ctrl F Propagate LV endocardium epi if next timeframe already has e Ctrl Shift F Propagate LV endo and epicardium forward and refine Ctrl Alt
8. if the ROI pen is selected You can also use the tools or to propagate the endocardium or epicardium respectively 12 3 4 Expand or contract segmentation If the shape of the contours is satisfactory but are inside or outside of the myocardial border the tools 4 or can be used to expand or contract respectively the contours The tools are applyed on selected slices and expand or contract the contour in a relative manner If the checkbox X Single Frame Mode is checked then the tool is only applied in the current time frame otherwise in all time frames 54 12 3 EDIT THE SEGMENTATION RESULT 12 3 5 Manually adjusting the contour by interpolation points Manually correction of the contou by using interpolation points is probably the easiest way to make changes in the segmentation This functionality is chosen by the two icons 2 and for endocardium and epicardium respectively If there is LV segmentation in the selected slice one left mouse click in the current slice will put interpolation points for the contour If no LV segmentation is present in the current slice a LV segmentation can be performed by the interpolation points by select or 2 tool Then add interpolation points by left mouse click and interpolate the contour by shift click The LV segmentation is then corrected by move the interpolation points by dragging with the left mouse button and hold it down New interpolation points ca
9. is used to manually draw the right ventricle RV endocardium The icon x is used to automatically delineate the RV endocardium Note that the RV tool is not as automated as the LV tools The icon is used to refine the RV endocardium The icon is used to put RV endocardial pins for guiding the automated RV segmentation The icon 4 is used to manually drag the 43 CHAPTER 10 PROGRAM OVERVIEW RVEPI Figure 13 Right ventricular toolpalette 10 10 3 Viability Scar tools The functions described in this section is in US only for off label use and for investigational use The viability tool palette is shown in Figure Bs lee Palo Figure 14 Viability toolpalette The icon is used to automatically delineate infarct region on MR delayed enhancement images The icon 2 is used to manually delineate infarction The icon 2 is used to manually delineate regions with microvascular obstruc tion The icon 4 manually removes infarction The icon erase manual corrections of infarction The show the manual interactions and regions of microvascular obstruction you need to press the key o to toggle the display 44 10 10 TOOL PALETTE 10 10 4 Miscellaneous tool mode The miscellaneous tool mode is shown in Figure Figure 15 Miscellaneous mode toolpalette The icon is used to place annotation points The icon EN is used to make length measurements Left click with mouse at the starting point and hold mouse
10. o ER Vs AS RR 44 4 Volume calculations o 2 2 Em nn 44 5 Mass calculations 2 CC m a ee aoe Be ee Bee ae ee hog te ye at a ee ee ee ee 44 8 Wall thickness 22222 Cm on nn IAEA 44 10 Infarct size extent and transmurality 44 11 Number of SD from remote for Scar 44 12 T2 T2 calculation implementation 44 12 1 Calculating fitting error 44 12 2 Smootkinp sme 2 4 a ehren 175 176 177 177 177 178 181 181 185 186 187 187 188 188 189 191 191 191 CONTENTS 44 13 Longaxis volumes Bibliography 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
11. 20 9 Find patient details in DICOM files Analog to the above function but instead looks in all your DICOM files The following heuristics is used to classify a file as DICOM or not e Files that ends with dcm e Files that only contains digits and no extension e Files with name that contains more than 7 dots and the two first letters corresponds DICOM identification of an imaging modality The output of this function is an Excel file where each line is one unique patient identity and the number of files in which the patient name was found Note that to be completly certain about the are no DICOM files with the patient details you need to count the number of files that are deleted anonymized for each patient or simply run the function twice 20 10 Export from multiple mat files This function summarize multiple mat files into one summary This is very useful for research studies For instance by placing mat files one for each patient in one folder It is possible to summarize all patient data into one Excel sheet Note that each mat file can contain several image stacks The program automatically determines what image stack is for instance short axis slices and what image stack is viability images If this automatic image stack detection fails it may be necessary to load the image stacks and select correct image type For further details see Section Currently the following data is outputed for each files File name Patient name Pa
12. 32 4 PERFUSION ANALYSIS 32 4 Perfusion analysis The automatic analysis of myocardial perfusion is work in progress and will be made freely available upon publication of these algorithms 32 4 1 Automatic quantification of stress induced ischemia and infarction To perform automatic quantification of stress induced ischemia and infarc tion both a rest and stress image stack need to be present For Segment to be able to identify the rest and stress image stack the Image Type has to be defined as Perfusion Stress and Perfusion Rest respectively The automatic quantification of stress induced ishcemia and infarction in SPECT images is performed by two steps First an image registration is performed between the rest and the stress image stacks Secondly segmentation and quantifica tion of the perfusion defects is performed by using the rest and stess counts the stress rest count change and the rest wall thickening if a gated rest image stack is present The following sections describe the two steps Image registration The image registration between the rest and the stress image stacks is per formed by use the function Auto Image Registration under the Perfusion and SPECT menu The registration method is based on statistical optimization and the result can therefore vary slightly each time registration is performed on the same image stacks To only show the registration result use the func tion Show Image Registration under the Per
13. 32 4 2 Automatic quantification of stress perfusion defect 148 32 4 3 Manual perfusion scoring 150 153 155 34 1 Velocity Encoded Imaging 155 arg ee ee ee ee 156 pea ah Sea oy ge 157 cee pum be ta 157 34 2 Tagging s ss 6 so amp c s amp roto Oe RES Km Ree OES 158 34 2 1 Automatic strain analysis 158 161 165 ee Tee ee e o e e ee ee 165 169 e464 8 248642424644 Be Sie 170 37 1 1 Read flesf 4 Oe a 8 ss rss ss ss ss 172 do BE a do ee er are 172 i ie a eek Se eo a ee 172 BAe dc A eee r ee Be ae aS 173 o a ee Be Yd a 174 Poe oR aeda hate 174 Cd Ree Ob RR ea ge 174 viii CONTENTS 38 Report Module del Configurationl s bia svs A A AA ee 38 1 1 Hospital logO 224 he band en an an dar 38 1 2 Reference Valles sesos as se a 38 1 3 Headings for textual report 38 1 4 Reviewing doctorl 4 4 2 2 a lt Se Gee ye dees 39 Short Commands Hot keys 39 1 Hot keys penr a ra ede a eed et od BR eed a 40 How to Reference the Software 40 1 Examples of possible formulations 41 Support 41 1 Submit bug report lt 4 4 ka ee sh area 41 2 Data privacy policy 22er a eae eo ae ae es 41 3 General support issuesl cos rss rss vs er 42 Segment User Community 43 Plugins 43 1 Image Loader Plugin 43 2 Image Calibration Plugin 22 551660645 220 45 44 1 Version handling
14. Below each image stack the user can manually select color map The two selections are gray and cool and can be different for the two image stacks To change the transparency in the fusion image stack hold the right mouse button down and move up or down In the anatomical and functional image stack the right mouse button will change the brightness up down and con trast right left Click on the left mouse button define the current slice in the image stack Same slices are always shown in anatomical and functional image stack The arrow buttons on the desktop can then be used to step in the slices in the last clicked image If the last click was in one of the co registration sliders the arrow key buttons will change the position of the slider The manually co registration of the functional image stack is done by chang ing the parameters in the right box in the GUI The three sliders and edit boxes on the top translate the image stack The sliders and editboxes in the middle make a rotation in the image stack The three radiobuttons below the sliders flip the image stack in x y and z direction respectively The Undo co registration button undoes the last translation or rotation It also undo the Reset all button This button reset both co registrations col ormaps current slices contrast and brightness in all image stack to the start values The Reset contrast button only reset contrast and brightness in the
15. DE MRDE al NM PT or cTheart ET US s US Figure 45 Example of a parse file for image description settings In this section we will only describe DICOM interpretations the other set tings are explained in conjunction with Segment Server documentation and Patient Database Module The DICOM interpretation adjusts how Segment interprets DICOM files The checkbox X Force 16 bit DICOM enforces Segment to assume usage of 16 bit DICOM files regardless what is stated in the file This option is helpful when images looks like chessboard when read into Segment For further details see about loading DICOM files in Chapter 9 29 3 PACS Settings PACS Settings are described in the Segment Database Manual 29 4 Technical details On Windows platform the preferences are stored under the local user folder and the subdirectory Application Data Segment This means that each user have can set their own preferences If you want to have it setup so that all new users on the computer will have a default setting of preferences then 132 29 4 TECHNICAL DETAILS r 2 Segment Advanced System and DICOM Preferences gt Database Settings C Users Nisse LundahNDocuments Source trunkiDatabase Segment Server Settings 104 DICOM port for Segment server MYCOMPUTERNAME AE Title of Segment Server prefer little Receive Options storescp Sending
16. Segment or by exporting the current image stack as a movie Export Movie 126 28 8 MOVIE RECORDER 28 8 Movie Recorder This is an experimental functionality that take screen captures and store them in a movie format The movies can be done in two ways and either to avi files or a sequence of png files that later can be converted to different file formats In future versions it will also be possible to export to animated gif format You can create movies of the main view zoom view 3D plot view report per slice view First select Movie Recorder under the Export menu This brings up a user interface shown in Figure Set output file C DatalimagedatalL VIMRimovieout te d Frames to recor 30 Figure 42 Movie Recorder GUI The movie recorder is when started unpopulated To do a first screen capture force an image update by view next frame You can now set a crop box shown in Figure 42 as a red box set number of frames to record and start to record the movie Usually you should set the number of frames to record to the same number of time frames as there are frames in the image stack When all frames are recorded then a file selection pop up menu appears and where you can select storing options When exporting to avi files you need also to select a movie compressor since all compressors might not be available on your computer Personal experiences are that the cine pak encoder are pretty stable 127 29 Custom
17. epicardium This is done by using the function Add RO s in sector selected slices You will be prompted for center angle width in degrees percent from the wall Zero center angle corresponds to three o clock and counting counter clock wise This function only adds sectors in selected slices An example of automatic ROI placement is shown in Figure Figure 25 Automatic placement of ROI s inside the myocardium Another possibility to create ROT s is to convert the endocardial epicardial or scar surface to a ROI This is done by the option Copy endocardium to a ROI Copy epicardium to a ROI or copy scar to a ROI This only includes the selected slices 18 2 Modifying and deleting ROI s By right clicking on a ROI a pop up menu appears where it is possible to 82 18 3 TRANSLATING AND SCALING ROP S e Delete ROI e Set ROI label change the name function of the ROT e Set ROI color change the color of the ROI e Copy ROI upwards e Copy ROI downwards e Copy ROI outline to all timeframes e Refine ROI for flow purposes see Chapter 23 e Switch ROI sign useful for flow analysis 18 3 Translating and scaling ROT s ROT are translated with the icon P and scaled with PK Point on ROI contour and drag while mouse button kept down to adjust to correct posi tion size 18 4 Deleting ROI s Under the ROI menu it is also possible to Delete ROI Delete ROl s Using Template and Clear All ROI s The fir
18. use the same approach as described above It is often advantagoues to first draw all the remote ROI s 102 21 4 EM ALGORITHM and then the scar ROIs since you do not need to alternate with labeling the ROT In a final step to use the method of standard deviations from remote you need to set the parameter Beta to zero To change the standard deviations from remote see under Technical details below 21 4 EM algorithm This automatic mode is developed for ex vivo studies In cases where it fails make necessary manual corrections by using the tools Land Y respectively It may be necessary to manually mark regions of microvascular obstruction to get these regions delineated The weighting mode should not be turned on for high resolution ex vivo CMR images 21 5 Technical details It is possible to control the parameter Beta Min volume Standard deviation from remote The parameter Beta controls the smoothness curvature forces on the level set surface and in practice it controls the smoothness of the result The parameter Min volume controls the minimum size allowed for an infarct in ml The parameter Standard deviations from remote controls how many standard deviations from remote that should be taken when calculating a slice based threshold The default for the automatic mode is 1 8 for the weighted algorithm and 2 4 for the SCJ method Generally this should only be changed when using the mode SD from remote These parameters
19. DICOMS Poa Send Options ume DICOM interpretation 7 Fast preview of multiframe slice DI ee ER ee San E Force usage of 16 bit DICOM A No ome Figure 46 Advanced and DICOM Settings GUI copy the preferences mat from one user to the folder where Segment is installed Finally make this file write protected In the preferences folder Segment also stores a log file for debugging purposes and small temporary files that are used in the PACS communication batchdownload process 133 30 Image Reformat MPR The functions described in this chapter is in US only for off label use and for investigational use It is possible to reformat an image stack along any axis The main purpose of this tool is to be able to resample the data volume to short axis slices if they are for instance scanned in an axial direction The reformater can also be used to construct a long axis image from a stack of short axis slices The user interface is shown in Figure One limitation with the multiplanar reconstruction is that it does not utilize the patient image coordinate system This means that image stacks created with the reformater does not display image plane crossings This will be addressed in future versions of Segment Furthermore the MPR routine does not currently support non isotropical voxels i e voxels of dimension 3x4x8 mm Voxels where x and y size are equal do work i e 3x3x8 mm works fine The functions are
20. F Propagata RV endocardium forward do not refine Alt F Propagate Flow ROI forward and refine Ctrl T Track tool for LV endocardium Alt T Track tool for Flow ROI Ctrl U Copy LV endocardium upwards and refine Ctrl Shift U Copy LV epicardium upwards and refine Ctrl Alt U Copy RV endocardium upwards and refine Ctrl D Copy LV endocardium downwards and refine Ctrl Shift D Copy LV epicardium downwards and refine Ctrl Alt D Copy RV endocardium downwards and refine Ctrl V Exclude papillary muscle from LV enocardium Space Toggle tool in toolbar menu depending on tool and mode Shift L Select LV mode Shift R Select RV mode Shift F Select ROI Flow mode Shift V Select Scar Viability mode Shift M Select MaR mode Shift I Select Misc mode Ctrl B Bullseye plot Ctrl N Load next mat file Ctrl 0 Load image stack Ctrl P Open patient data base Ctrl Shift G 182 39 1 HOT KEYS i Reset GUI Position Ctrl S Ctrl W Shift Ctrl W Ctr1 Q Ctrl Z Ctrl plus Ctrl minus Mouse wheel Shift Mouse wheel Ctrl Mouse wheel Alt Mouse wheel Save all image stacks Close current image stack Close all image stacks Quit program Undo segmentation Zoom in Zoom out Scroll through slices Scroll through time frames Scroll through visible thumbnails Zoom 183 40 How to Reference the Software To be permitted to use the software for research purposes you need to ref erence the usage of the software properly for more details see Chapte
21. If your previous version used another MCR then you need to first replace your old Matlab Compiler Runtime To see which version of Matlab Com piler Runtime is required please see the table below Segment version MCRInstaller lt 1 675 Matlab Compiler Runtime 7 6 1 8 Matlab Compiler Runtime 7 8 1 9 Matlab Compiler Runtime 7 15 2 0 Matlab Compiler Runtime 2014a If you need to upgrade MCR follow the installation instructions in sec tion It is important to uninstall the old MCR before installing a new one When having problems installing or uninstalling the MCRInstaller please consult Mathworks support pages and search for MCRInstaller If you as in most cases do not need to upgrade MCR simply download the Segment installation file and double click on it to install it as described in section 8 1 2 8 5 First time running Segment Doubleclick the file C Program Files Segment Segment exe or your short cut to it to start the program The first time it is started it runs a setup process which can take a while so be patient To complete setup set pref erences and window positions as described in Sections and 8 5 1 Setting preferences It is recommended to set the preferences of which folders to use to avoid browsing each time you want to load or save a file It is invoked by using the Preferences on the main menu Set Data Export and CD folders The preferences are saved as a file segment_preferences mat in a folder th
22. Section which allows quantitative studies of wall motion abnormalities Further hints on doing stress analysis is to label your image stacks Then it is easy for the viewer to see which image stack is stress and which is rest This is done by right click on the image thumbnail and select Set Image Type in the pop up menu 119 26 Regional Wall Analysis There are a number of different analysis options available to make regional wall analysis Please note that for regional wall motion analysis the com mon clinical practice is to exclude the papillaries from the segmentation for more information on how to include exclude the papillaries see Section 12 3 There are three different visualization options available for wall motion anal ysis e Radial contraction versus time e Report per slice icon ES e Bullseye plots icon 26 1 Radial contraction versus time In this option the regional contraction velocity per segment is plotted over time On the y axis on each plot is the slices basal to apical and on the x axis is time An example is shown in Figure 26 2 Report per slice It is possible to do regional wall motion analysis on a slice by slice basis This tool is started by the icon EX Possible parameters to plot are wall thickness fractional wall thickening radial contraction velocity and radius An example showing wall thickness over time is shown in Figure AT You can adjust the start of the sectors by using the rota
23. The functions described in this chapter is in US only for off label use and for investigational use This module is useful for delineating complicated 3D anatomical objects Since it is less specialized than the segmentation of the left ventricle it is less automated The functions described in this chapter is in US only for off label use and for investigational use Promising new techniques such as prototype based image segmentation has been incorporated in this module Section 15 9 15 1 Viewing data The graphical user interface is shown in Figure 22 There are three orthogo nal views and one view of the speed image further described in Section 15 2 2 The slice position of the upper right image is shown as a red line in the two other slices The leftmost lower image and rightmost lower image are shown as green and blue lines respectively When the selection tool is active then by left click in any of the three orthogonal views the postion of the im age planes can be adjusted There are four checkboxes that control how the data is displayed When the checkbox X as MIP is checked then the shown image is a MIP image Maximum Intensity Projection Note that contour overlay is not done in the MIP projection The checkbox amp Interaction shows manual edits and region growing interactions Placed seed points and added areas are shown in green and removed areas are shown in blue The checkbox X Selection shows the segmented objec
24. The icons P and zooms in out the current active image stack The icon e refreshes the screen which might be very useful since it also refreshed the GUI which under certain circum stances might hang in case of calculations that went wrong If the GUI seems irresponsive it is well worth to try refresh the screen The icon resets the light contrast setting The icon Xo automatically sets which sets contrast and brightness so that an upper and lower percentile of the inten sities get saturated The icon undo the latest contour editing command The icon Lil shows information about the current image stack 10 2 Montage view Figure 9 shows a screen shot of the program in the most common view mon tage view selected by the icon H You can also switch between the montage view and the single slice view by using the hot key v In the montage view all slices in an image stack are displayed The slice s with a yellow box around are selected Automated segmentation and many other operations are only applied to selected slices Slices are selected by activating the tool and by left mouse click on the desired slice and drag the mouse while the left button is hold down 10 3 Montage row view The montage row view is same as the montage row but with the difference that the slices are shown to minimize the number of rows that are used to display the entire image stack 10 4 One slice view In one slice view only one single slice are
25. Y Hsu A Natanzon P Kellman G A Hirsch A H Aletras and A E Arai Quantitative myocardial infarction on delayed enhancement MRI Part I Animal validation of an automated feature analysis and combined thresholding infarct sizing algorithm J Magn Reson Imaging 23 3 298 308 2006 R J Kim D S Fieno T B Parrish K Harris E L Chen O Simon etti J Bundy J P Finn F J Klocke and R M Judd Relationship 201 BIBLIOGRAPHY 10 11 12 13 202 of MRI delayed contrast enhancement to irreversible injury infarct age and contractile function Circulation 100 19 1992 2002 1999 J B MacQueen Some Methods for classification and Analysis of Mul tivariate Observations In Proceedings of 5 th Berkeley Symposium on Mathematical Statistics and Probability volume 1 pages 281 297 Berkley 1967 University of California Press J Sjogren J F Ubachs H Engblom M Carlsson H Arheden and E Heiberg Semi automatic segmentation of myocardium at risk in T2 weighted cardiovascular magnetic resonance J Cardiovasc Magn Reson 14 1 10 2012 A Chernobelsky O Shubayev C R Comeau and S D Wolff Baseline correction of phase contrast images improves quantification of blood flow in the great vessels J Cardiovasc Magn Reson 9 4 681 5 2007 C M Wacker M Bock A W Hartlep G Beck G van Kaick G Ertl W R Bauer and L R Schad Changes in myocardial oxygenation and perfusion
26. anatomical and functional image stack and the transparently in the fusional image stack to initial values If you need to fuse many data sets with approximately the same parameter settings the default buttons can be helpful The Save as default button saves the current translation rotation flip and colormap choices These settings are then available to use on another data set The settings are applied to the image stack by using the button Apply default When you are satisfied with the fusion use the Ok button This results in a new image stack with image type Fused and contains the functional images 162 stack with the anatomical image stack size and the segmentation from the anatomical image stack Example of such an image stack are shown in Figure The parameter settings are also saved and the fusion GUI with the old parameter choices can be open again by select Fusion of Two Image Stacks under the Fusion menu when having an image with image type Fused se lected When an image stack with another type than Fused is selected a new fusion GUI always open Pushing the always result in a new fused image stack Ok button in the fusion GUI Figure 62 Example of a fused image stack 163 36 Perfusion Analysis The functions described in this chapter is in US only for off label use and for investigational use The perfusion modu
27. and quantified under pharmacological test in coronary artery disease 11 quantification of iron overload and of the heart and liver in Thalassaemia major 12 T2 values can be quantified by varying when the same image is acquired using different echo times 31 1 Module overview An overview of the T2 T2 quantification module is shown in Figure The top left image panel shows the magnitude images for the different echo times adjustable with the echo time slider The lower left panel allows to make regional restriction on what regions to quantify There are three modes and in the first mode Use only myocardium the pixels inside the myocardium is included in the quantification The second mode Use only ROI includes only pixels that are inside region of interests In the last mode Use full image all pixels are included in the quantification The delineation of ROT s and myocardium is taken from the last time frame in the image series The right image panel shows the pixelwise T2 values 137 CHAPTER 31 T2 T2 QUANTIFICATION MODULE Fr 5 cr ROI T2 36 87 ms Cl 32 3 49 2 ms CoV 12 99 regions Echo time image stack ROI fit SI au 0 5 10 15 20 25 TE ms Echo Time Frame 8 gt Parameter map ae Pixelwise T2 T2 map T2 ROMt Display limit 60 ms fl gt j Pixelwise residual error map T2 pixel fit Error threshold 15 126 gt j Regional Restriction Cre
28. are also a few modules that are not yet available to the research community but will be made freely available when we have published meth ods paper describing the adequately Strain analysis from velocity encoded MRI images T2 Module Automated whole heart segmentation of CT images Automated bone segmentation of CT images Volume Rendering Module 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 Johan
29. as WT RR ae ELER 3 Where WT is fractional wall thickness and WT is wall thickness and WT gp is wall thickness in end diastole In the bulls eye plot then fractional wall thickening is showed in end systole 196 44 9 CALCULATION OF REGURGITANT VOLUMES AND SHUNTS 44 9 Calculation of regurgitant volumes and shunts The regurgitant fraction for the aortic valve and the pulmonary values are calculated as v r 100 4 4 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 Vforwd 100 E SV 5 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 QrQ 6 44 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 setti
30. assumption Note that this auto detect should be disabled when manually drawing contours For further details see Section 12 1 2 If the checkbox amp Single frame is selected then segmentation and other opera 33 CHAPTER 10 PROGRAM OVERVIEW Number of viewing panels Viewing preferences Adjust view i Report tools Quantification Long axis motion Volume curve Toolbar Palette Thumbnail Main viewing area Segmentation preferences preview Figure 8 Main graphical user interface 34 10 1 VIEWING IMAGE STACKS tions such as translate scale and delete are only applied to the current time frame To further make the user aware of this change of behavior the box around the currently selected image panel turns to white when single frame mode is selected 10 1 Viewing image stacks To view a non visible image stack simply drag the thumbnail to an image panel Right clicking on the thumbnails brings up a context menu where more options are available To view all loaded image stacks press Shift A Only one of the image stacks are active at the same time Around the active image stack an orange rectangle is drawn both in the main image drawing area and around thumbnail image Image stacks can be viewed in four different modes one slice view montage view montage view in rows and m mode view The different modes are selected with the ic
31. cine images ES shows both cine images and the cor responding short axis delayed enhancement images shows cine delayed enhancement and perfusion images shows a stress display I shows a flow view with a magnitude and a phase contrast image to the right This mode is subject for future improvements 10 12 General view and reporting functionality The report tool Ed creates a full text and graphical report of all the measure ments for all image stacks The icon Y starts a movie recorder that allows to 46 10 12 GENERAL VIEW AND REPORTING FUNCTIONALITY store an image stack as an avi movie It is also possible to directly export a movie under the Export menu There are seven tools available to visualize or handle image stacks Each of these starts separate graphical user interfaces to view and manipulate image data They are all available as icons on the main menu The icon l starts the general segmentation tool described in Chapter The icon Y starts a tool to do multiple planar reconstructions described in Chapter 30 The icon 5 starts the Image Fusion Module The icon starts a three dimensional visualization tool and an example of a such visualization is shown in Figure The icon starts a volume rendering tool This tool is under development and currently unavailable The icon FX starts a tool to do regional wall motion per slice analysis described in Section 26 2 The icon starts a tool to do bullseye visualization of
32. e SD from remote Implementation of taking two 2 SD from remote my ocardium as proposed by Kim et al 7 You need to place ROI s in the myocardium and label them ase remote e K means Using the k means algorithm with two normal distributed classes infarct and non infarct Original algorithm described by 8 e EM algorithm Using the EM algorithm with two normal distributed classes infarct and non infarct as described by Each of the different methods are further described below 21 1 Automatic mode weighted SCJ or FWHM The automatic mode is the default mode In cases where it fails make neces sary manual corrections by using the tools and Y respectively Note that including extraneous black regions in the weighted method only marginally 101 CHAPTER 21 VIABILITY ANALYSIS changes the result since the infarct is weighted with pixel intensity In the weighted method it may be necessary to manually mark regions of microvas cular obstruction to get these regions weighted correctly 21 2 Manual mode In this manual mode the infarct area is not automatically updated and the only way to change the delineation is by doing manual interactions If you want to start from scratch to manually draw your infarct regions then first select Clear all scar data This option also resets the viability mode to Auto matic mode so you need to choose Manual mode before starting to draw the infarct regions 21 3 SD from re
33. gives YSize e IM SIY gives XSize e From the element IM_SIZ and IM_SIT a temporarily zsize and tsize are extracted If this information does not match the previously ex tracted information for number of slices and number of timeframes then the number of timeframes are calculated as zsize divided by the previously extracted number of slices from the reco file If the newly calculated number is not a valid number of timeframes then the num ber of timeframes is taken from tsize 37 1 6 Parsing IntraGate info file Depending on if the scanner is an IntraGate Bruker scanner this file may exist If it is existing then the following information is read from the file e par heartrate this element gives the heart rate of the subject HeartRate e par heartsignalDuration this element is combined with par heartframes to get the time increment between each timeframe TIncr e par heartframes is checked against number of previously detected timeframes and an error is issued if there is a mismatch 37 1 7 Reading timing information Unless for the IntraGate scanner the timing information time increment between timeframes TIncr is taken as the repetition time if present and otherwise taken as the echo time 174 38 Report Module This functionality is only available in the clinical commercial version of Seg ment The report tool is a report generator is a tool to generate reports of a study The tool is started by
34. image it is This might be required for future analysis in some applications It is also a good idea to label image stacks upon loading when for instance doing stress analysis to be able to safely differentiate baseline from stress exams For research purposes it is possible to set free text name as Image Type and Image View Plane e Select the desired region of interest size Usually for normal hearts 100mm is sufficient to cover the left ventricle Enlarged ventricles will need 150mm or even more e Click Load to start the loading process This brings up a red box in the preview image Position this box with the mouse and left click to start the loading process If you want to use a different size of ROI right click to abort loading operation Then click again on the button e Once positioned the box left click with the mouse to start loading the files Once all image files are loaded a dialog box opens where you need to con firm voxel spacing and timing details How Segment interprets the DICOM information to calculate these parameters is described in Section For users that do not use images from the three major vendors Siemens Philips or GE should read this section Further technical details about how Segment interprets the DICOM files are given in the Segment Technical Manual If heart rate is not present in the DICOM file Segment tries to guess that based on the time increment and the number of time frames to get R R
35. in most cases e NSLICES gives the number of slices Please not that is read as safe guard if the other files are missing This value will be overwritten in most cases e ACQ_slice_orient gives ImageViewPlane e ACQ_inversion_time gives InversionTime e ACQ_scan_name gives SeriesDescription e ACQ method gives ImagingTechnique 37 1 4 Parsing reco file The following elements are read from the reco file e RECO_size gives the reconstruction size of the image YSize XSize and if there are multiple slices also ZSize If this vector only contains two elements then ZSize is taken as the number of elements in the RECO transposition otherwise it is taken as the third element of RECO_size e From the element RECO_fov the pixel size is taken If this element contains three number then this information is divided with the number of slices to get SliceThickness e The number of images is extracted from the number of items in ele ment RECO_globex From this the number of time frames TSize is calculated a number of images divided by the number of slices If this is not a valid number of time frames then the number of frames is set to 1 Please note that this information is updated when reading the d3proc file 173 CHAPTER 37 NATIVE BRUKER READER MODULE e The bit depth of the 2dseq file is taken from the element RECO_wordtype 37 1 5 Parsing d3proc file The following elements are read from the d3proc file e IM SIX
36. installation of Segment Then you do not need to install MCRInstaller 19 CHAPTER 8 INSTALLING AND UNINSTALLING on each machine that is used to run Segment Make a network installation of MCRInstaller How to do this shown in this document www mathworks com access helpdesk help toolbox compiler f12 1000291 html Thereafter place Segment in a network folder and make sure that each user can find Segment exe 8 2 Installation for source code version Please note that currently is not Linux 32 bit supported but Linux 64 bit are supported We will at a later stage also support Linux 32 bit but it is not easy trying to keep all platforms up to date Install Segment by 1 Download zip file see download pages 2 Unzip the file and store contents in directory 3 Installation complete Starting by 1 Start Matlab 2 Change directory to where you have unpacked Segment 3 Type segment at Matlab command prompt 8 3 License file If you have received a license file then your version is registered full version then copy your license file to the same folder as where segment is installed The license file is called yourname key or license key If you do not have a license file then the program will run in Research only mode fully functional where only a few options are disabled You may then not use the software for commercial research or clinical routine 20 8 4 UPGRADING SEGMENT 8 4 Upgrading Segment
37. interval This will fail if your image sequence is for instance one image every heart beat 28 9 1 LOADING DICOM FILES 9 1 4 Tips and tricks Often the files are not stored exactly as prerequisited above then there are many tips and tricks available e You may select several subfolders Then the program loads all the files in the subdirectories Each subdirectory must have the same number of files This is the case for old Siemens files and Bruker Paravision DICOM files e You may select what DICOM files to load directly Note however that the files need to form a valid image stack and the result may be incorrect if slices are missing etc When you do this always ensure that the files are sorted properly e It is possible to preview different files by the Position slider e To get detailed information about DICOM tags in the files press DICOM info 9 1 5 Loading images from CD When loading images from a CD it is highly recommended to import the files from the CD to your image data directory This is done by using the utility described in Section 20 5 9 1 6 Graphical image series selection The graphical series selector tool is shown in Figure While moving the mouse pointer over the image series more information on each image series is shown in the top of the graphical interface Select which image series to load with left mouse button Image series outlined in yellow are selected It is also possible to gr
38. it is recommended to set this to quite small typically 1 2 The edit box Number of Points Along Contour sets the number of points that are stored along a contour for endocardium and epicardium When us ing automated segmentation this value should be set to 80 When manually drawing complicated objects this can be set to a higher number If the op tion amp Blind Subject Identity is checked then the program will not show patient info on screen this is useful for making screen shots etc for presentations It is highly useful when doing research and the observer should be blinded to the patient identity The edit box Number of visible thumbnails sets the maximum number of thumbnails visible When the number of image stacks exceeds this number a slider will be visible to scroll through all the thumb nails The radio buttons Radial profiles from endo epicardial centroidcon trols how regional wall measures are placed The radio button Modified centerline method is reserved for future use when the modified center line method will be implemented The edit box Number of radial profiles to evaluate sets the number of radial spikes that are evaluated before sector means are calculated For more details on how the regional parameters are calculated see Chapter 44 The checkbox X Include touched pixels in ROI sets how the edge pixels of a ROI are treated When selected all pixels that are touched by the ROI are included The default be
39. load a segmentation select Load Segmentation under the File menu The current limitations of this operation is that you should not have removed reordered any slices compared to when you saved the file This limitation might be removed in the future When loading some elementary error check ing is done to ensure that the loaded segmentation indeed was done on the same image stack To disregard this safety check see importing segmentation below 16 3 Importing segmentation result The difference between loading and importing segmentation is that the error checking is disabled This means that it is possible to load a segmentation from another dataset and overlay that on the current image stack This could be especially useful for instance with late enhancement image where the delineation can be performed on gradient echo and SSFP cine images and then be overlaid on a late enhancement images See Section on details how to translate the segmentation loaded segmentation 16 4 Hints Setting the data path and export path in the preferences menu see Chap ter 29 saves a lot of work when frequently loading or saving images When 72 16 4 HINTS performing studies where the observer should be blinded to the identity of the patient you can use the option to hide patient ID when loading the images For more details see under Chapter 29 73 17 Image Tools The functions described in this chapter is in US only for off label use and f
40. lt 76 17 5 1 Permanently apply light setting 76 E ok E Pe A i 76 17 5 3 Invert colors or AA er 76 a Ano ee e Gee we Ge 77 17 5 5 View intensity mapping 77 iv CONTENTS 17 5 6 View true image intensity TT 17 6 Set colormap for current image stack 2 2 2 2 TT 17 7 Flip Rotate image stack 2 2 2 4 eed ns evden nes 77 17 8 Resample image stack 2 2 sr mn nen 78 17 8 1 Reformat multiplanar reconstruction 78 SEA 78 oe 78 17 9 Add noise aa rr rr rr A ee A 79 Laia ere er 79 EEE a EN 79 er ees ee eg ae ee ee 79 ee BSG A owe BH 79 Coke om Re a ee ee 79 E A 80 AA ee ee ee 80 17 17 Remove subject identity 80 ie Re de ee ee 80 81 Sia HR Gy ie eet es Ge ee ee eee 81 oe eH enh ee AE 82 ed Boa eo ee 3 83 Ou pod Roe OR de OU CR ee 83 pe ue be ee ee ee a a DR 83 ee ee eee ee ee ee ee 85 be es Se ee ee EE 85 19 Measurements and Annotations 89 fe Rk HO ee HR ee ee 89 TER PA ee ge es A ew A re Be Be Soe Ba 89 19 3 Vols 2 5 5 8 4 4 5 RS SSS SS is RS 90 OA Areak ah Bs za gr BS a eS EE ER SS oe a 90 19 5 Flow and volumes 4 rer rr ea 91 19 6 Signal intensityl Gy koh bea ee be REE REESE 91 19 7 Annotation and anatomical landmarks 91 CONTENTS 20 Utilities 20 1 Anonymize DICOM files Recursively 20 2 Anonymize mat files Recursively 20 3 Clear
41. protected by copyright law and international treabes Copyright 1984 2011 The MathWorks Inc MathWorks Figure 4 Click on Next the file where you easily can find it i e your desktop When downloaded double click on the file and follow the instructions You will be prompted if you want to install the program to the default location C Program Files or C Program depending on operating system language One advantage of installing to another location where you have write access is that you can thereafter install upgrades without being logged in as local administrator 8 1 3 Create shortcut Place a shortcut to the file C Program Files Segment Segment exe at your desktop Note that depending on your system locale or if you have installed Segment to a non default location this path may be different Cre ating this short cut is done by using the standard Windows file explorer to find the file then right click on the file and select the option Create a short cut Move the created shortcut to your desktop 8 1 4 Notes for Windows Vista users You will need to run the application in administrator mode the first time you run Segment since the first time Segment is started some files are extracted This operation is blocked in user mode The second time you run Segment you should be able to run in a user mode 8 1 5 Network installation of Segment For advanced users and system administrators it is possible to make a net work
42. serie e 2dseq file This file contains the image data for each image serie Each file may have the optional ending txt 37 1 2 Parsing the subject file The first step of loading Bruker files is to select a subject file The following parameters are read from the subject file e SUBJECT_id is parsed to Patient ID e SUBJECT_name_string is parsed to Patient Name e SUBJECT_dbirth is parsed to Patient Birth Date e SUBJECT_sex is parsed to Patient Sex Here the string female not case sensitive is mapped to F and male is mapped to M All other strings are mapped to e The patient age is not read from the subject file and is set to empty Reason for not reading that is that we have not found files containing this information 37 1 3 Parsing acqp file The following data is read from this file e ACQ spatial size from this vector the two first elements are taken as YSize and XSize respectively e ACQ_flip angle gives FlipAngle 172 37 1 IMPLEMENTATION DETAILS e ACQ_slice_thick gives SliceThickness Please note that this infor mation is read as safe guard if the other files are missing This value will be overwritten in most cases e ACQ_echo_time give EchoTime e ACQ_repetition_time give RepetitionTime e ACQ_trigger_delay give TriggerDelay e ACQ n movie frames give the number of timeframes TSize Please not that is read as safe guard if the other files are missing This value will be overwritten
43. than this value are included in the MaR segmentation process The Minimum volume number determined the smallest volume for a defect expressed as percentage of the LVM the default value is 10 All defects with a volume smaller than this number are excluded from the MaR segmentation The two selection for the subdivision of the LV used in the a priori model are the default model based on normal coronary artery perfusion territories and the standard 17 segment model The choice in the lowest panel determine if the a priori model of the coronary distribution should be used in the MaR segmentation or not 2 SPECI DefectiPreferences m SPECT Defect Preferences gt 5 Apply setting to pixels in ROI stack O Image stack Count Maximum Percentile of pixels 100 the single hotest pixel 100 100 Threshold Percent of Count Maximum which defines a defect 55 35 Minimum volume to be identified as defect 10 10 Division of the Ly Default model 17 segment model Using a priori model With model Without model Figure 53 The MaR preferences interface 32 3 3 Reset MaR To reset the MaR quantification use the function Reset MaR under the My ocardium at Risk and SPECT menu This function reset both the MaR seg mentation and the MaR preferences for the current image stack 146
44. the icon or under the Report menu The graphical user interface is illustrated in Figure The report can be generated in one of three formats e HTML format The Generate HTML report is used to generate a HTML report complete with images and plots Each page can be printed and together they contain a detailed report of an exam An example of the final output is given in Figure e JPEG format A simplified graphic report containing only text and tables can be created using the Send to PAF button This report is saved as a collection of JPEG files for easy upload to PAF The output folder can be set in the Advanced System and DICOM settings under the Preferences menu e DICOM format The simplified graphic report can also be saved as a collection of DICOM files and automatically uploaded to PACS by clicking the Save to PACS button Hospital logo patient data signature field and current date are automatically included in the report The checkboxes are used to select which details of the analysis are to be included in the report A checkbox is grayed out if data is unavailable e LV Analysis this section contains a table of global LV parameters and if the images are time resolved a volume curve e RV Analysis this section contains a table of global RV parameters e Scar Analysis this section contains a table of data from scar analysis and an image of scar delineation e
45. to not use the predefined startindex and or parameters by unselecting the checkboxes X startindex and X parameters in the Prototype panel To adjust the speed image push the button Adjust speed map The speed image for prototype based segmentation differs in several ways from the usual levelset segmentation The image is automatically intensity adjusted which can be seen by the magnitude image being Prototype adjusted The histogram is calculated from the adjusted magnitude image The speed mapping mode 68 15 9 PROTOTYPE BASED SEGMENTATION is Prototype shaped and the shown function is a probabilistic fucntion stored in the prototype Finally the Lambda slider and edit are enabled this controls the influence of the spatial map The spatial map is an a priori mapping stored in the prototype which constrains the segmentation The default value of the parameter lambda is also stored in the prototype The speed image shown is calculated from the speed mapping and by subtracting the spatial map If any adjustments need to be done it is possible to change the Offset and Zero level but firstly try to adjust the factor Lambda since the most important part of the prototype based segmentation is the spatial map When pressing the button Spatial map the spatial map is shown in a separate window When satisfied with the speed image press Dismiss To do the segmentation press eit
46. to plot the radius and diameter over time The radius are calculated as what diameter need a circular vessel have to have the same area as the area of the ROI The option Signed Kinetic Energy calculates the kinetic energy in the blood assuming standard density of the blood The final possibility is to plot a 3D profile of the velocity distribution of the vessel This can be plotted for all time frames at once or only a single time 109 CHAPTER 23 FLOW ANALYSIS frame that later can be stepped forward backward in time An example of the 3D plot is shown in Figure Flow plotting utility HER IT T Parameter to plot Aortic ascending flow Volumes ml Int between red bars Aortic ascending flow Tot47 289 Forward 49 55 Backward 2 2704 Figure 34 Example of plotting of backwards and forward flow simultane ously The sum of the two curves will be the net flow showed in Figure 23 3 Compensating for eddy current effects To get accurate flow measurements it is important to compensate for con comitant field effects such as eddy currents and Maxwell effects Ideally Maxwell effects should be compensated for directly on the MRI scanner since it can be analytically calculated Consult your MRI vendor for details about how this is implemented in your scanner Note that when compensating for eddy current effects the image stack should not be cropped upon loading since the algorithm ne
47. used in Segment The Positive slope is useful to segment regions that are brighter than a certain image intensity and the Negative slope is useful to segment regions that are darker than a certain image intensity The Prototype shaped speed mapping mode is further described in Section 15 9 The mapping is translated by adjusting the Offset slider The default behavior is that the mean signal intensity is used as zero level of the speed intensity mapping This is useful since after selecting seed points only small adjustments of the Offset slider is the usually required By unchecking the checkbox Intensity from seed as offset the zero level will instead be 0 5 The slope of the map 63 CHAPTER 15 SEGMENTATION OF GENERAL OBJECTS ping is adjusted by usage of the Width slider When pleased with the settings on how the speed image is calculated press Dismiss Histogram Magnitude image 1 true 0 8 otot 0 6 0 4 0 2 0 R 0 0 2 0 4 0 6 0 8 1 Normalized magnitude i Expand aj Slice Speed mapping Expand f 7 Zero SIE SERA RASER Aase Zero Contract 0 0 2 0 4 0 6 0 8 1 Normalized magnitude Gaussian shape Positive slope Contract Negative slope V Intensity from seed as offset 0 Al i gt Offset Defaut 03 4 p Wath Defaut Dismiss Figure 23 Graphical user interface to adjust speed image 15 2 3
48. you re probably already a top down learner your self However if you re a bottom up person don t despair If you have patience enough to ready only one chapter then read Chapter If you then get stuck you may use this manual to search for specific solutions Most of the icons and pushbuttons in the software have tooltip strings attached to them Simply point the mouse over a button and you will have feeling on what purpose it has If you do not want to read the manual at all you can instead see the on line video tutorials They are available under the Help menu 6 Conventions and Abbreviations This chapter describes the typographic conventions and used abbreviations in this manual and in the program 6 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 6 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
49. CMR Scientific Sessions 2008 M Ugander H Soneson H Engblom J van der Pals D Erlinge E Heiberg and H Arheden Quantification of myocardium at risk in myocardial perfusion SPECT by co registration and fusion with delayed contrast enhanced magnetic resonance imaging an experimental ex vivo study Clin Physiol Funct Imaging 32 1 33 8 2012 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 Feature 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 IEEE Computers in Cardiology 2005 volume 32 pages 599 602 Lyon France 2005 E Heiberg H Engblom M Ugander and H Arheden Automated Calculation of Infarct Transmurality In IEEE Computers in Cardiology pages 165 168 Durham USA 2007 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 H Engblom E Hedstrom F Bouvier P Sorensson J Per now H Arheden and E Heiberg An automatic method for quantifica tion o
50. GE for eddy current compensation For usage see paper by Alex Chernobelsky et al TO 23 4 Phase unwrapping In cases were the velocity in the blood is higher than the VENC the veloc ities can wrap around Under certain conditions these phase wraps can be uncovered and phase unwrapping can be performed to retrieve the correct ve locities The graphical user interface for the phase unwrapping tool is shown in Figure The checkbox amp Show ROI pixels shows the pixels that are used in the ROI in a red color This is useful when one want to know exactly what pixels are included in the ROI The checkbox X Use magnitude mask is used when one want to limit the automated phase unwrapping only in pixels that have a magnitude over a certain threshold 23 4 1 Automated unwrapping The automated phase unwrapping algorithm works on a pixel by pixel basis and operates along the temporal dimension It looks for pixels where the phase appears to have wrapped once up and once down Therefore the algo rithm will fail for a biphasic velocity profile if phase wrapping occurs at both phases Furthermore it only considers single wrap arounds i e the phase is assumed to have wrapped once 23 4 2 Manual unwrapping There are four tools available A t The tool is used to pan the images The second tool wraps the pixel up at left mouse button clicks The third tool wraps the pixel down at left mouse button clicks Th
51. MaR Analysis this section contains a table of data from myocardium at risk analysis 175 CHAPTER 38 REPORT MODULE r E Report sheet generator Se Components to include Y LV analysis Y 2CH Longaxis image RV analysis 7 3CH Longaxis image Scar analysis V 4CH Longaxis image Reference values Maceira Females Age 20 29 Maceira Females Age 30 39 Maceira Females Age 40 49 Maceira Females Age 50 59 Maceira Females Age 60 69 Maceira Females Age 70 79 m MaR analysis g E Shortexis image Maceira Males Age 20 29 Y Flow analysis Maceira Males Age 40 49 7 Shunt and Valve analysis Distance measurements Comments PATIENT HISTORY a lt Enter text here gt GENERAL IMPRESSION LV function lt Enter text here gt RV function lt Enter text here gt FINAL COMMENTS lt Enter text here gt Patient info Generate HTML report Send to PAF y Send to PACS Reviewing doctor Dr Bunza il Figure 67 GUI for patient report generator Flow Analysis this section contains flow data from phase contrast im ages and a plot of net flow over time If there are several image stacks containing different flow data one section will be added for each such stack Shunt and Valve analysis this section contains the Qp Qs ratio and regurgitant volumes and fractions for the mitralis and tricusp insofar as the data necessary for calculation is available
52. PECT Analysis Module is work in progress and therefore are not all automatic analysis tools currently freely available The SPECT analysis module can be used in both gated and non gated image stacks for analysis of left ventricular mass and volumes quantification of stress induced ischemia myocardial infarction and myocardium at risk To use the automatic analysis tools the Imaging Technique has to be defined as NM 32 1 Visualization In addition to the regular view of image stacks within Segment there are two visualization views specific for SPECT images By using Plot 2D View under the SPECT menu a seperate graphical user interface is opened with three short axis slices one basal one midventricular and one apical slice and horizontal and vertical long axis projections The user interface is shown in Figure 9 In the left panels the stress image stack are shown and in the right panels the rest image stack For Segment to be able to identify the rest and stress image stack the Image Type has to be defined as Perfusion Stress and Perfusion Rest respectively By using the and buttons in the lower panel the LV segmentation for each image stack can be manually corrected by include exclude basal or apical SA slices in the LV segmentation For gated image stacks the visualization is time resolved and the left ventricular blood volume is illustrated as a curve over time to the right in the interface A three dimensional view of the counts with
53. SK tool Scaling 99 CHAPTER 12 SEGMENTATION OF THE LEFT VENTRICLE can often successfully be combined with the refine operation 12 3 9 Manually include exclude papillary muscles One approach to remove papillary muscles is to perform a few iterations with the refine tools for the LV segmentation according to Section The papillary muscles can also be included excluded in the LV segmentation by using the manual drawing tools according to Section 12 3 6 12 3 10 Removing segmentation result The segmentation result can be removed with the right mouse click pop up menu shown in the place pin section above These function are also available in the main menu under Segmention 56 13 Segmentation of the Right Ventricle The right ventricle is much more geometrically complex than the left ventri cle The walls are much thinner and there are more and complex trabecula tion This is one explanation that there are currently in Segment no really good automated tools to do segmentation of the right ventricle This will be improved in future versions of Segment Currently what is available are the same basic functionality as for the left ventricle For the mid ventricular slices the automated methods manual draw refine can be used At the current stage we do not recommend to do time resolved segmentation of the right ventricle since the drawing and edit tools are so poor We would the suggest to remove all RV segmentation except sy
54. STRAIN ANALYSIS MODULE In a file that consist of velocity encoded image stacks with calculated strain in all the three long axis views it is possibly by clicking the icon of a bullseye plot to produce a bullseye plot of strain The function Export From Multiple mat Files under the menu Strain From Velocity Encoded Imaging under the Strain menu export strain values to clip board in all mat files in the selected folder 34 2 Tagging Imaging The strain tagging analysis module uses tagging MR images to calculate myocardial strain The module has been developed in close collaboration with researchers at KU Leuven in Belgium 34 2 1 Automatic strain analysis 1 The automatic strain analysis starts upon loading a tagged image stack Segment identifies a tagged image stack according to the DICOM tag Series Description The associated Series Description names can be customized by the user according to Section 11 2 The strain analysis starts by cropping and upsampling of the image stack if needed as shown in Figure 3 The automatic strain registration is then performed in the background The progress is shown in a progressbar at the bottom of the main interface of Segment During the registration process the user can perform LV segementation and open the strain analysis interface The LV segmentation should be performed in the first time frame or within 7 time frames from first time frame in the tagged or potential cine image stac
55. Start the segmentation tool Start the segmentation process by first draw some seed points regions by selecting the draw tool 4 The thickness of the pen can be adjusted by the slider pen radius The pen draws a sphere of the radius set by the slider in all three or four dimensions so you need to start to think and work three dimensionally If the checkbox X Manual interaction is checked then added re gions with amp is colored in green and removed regions with the tool G are colored blue By using the tool Pit is possible to remove user interactions created with the two tools Z and 4 respectively 64 15 3 MANUAL INTERACTION After drawing some seed points adjust the speed image such as the desired object s is shown in a red or bright yellow color This is described in detail in Section 15 2 2 above The user interface is started by the Adjust speed map This adjustment is rather critical for the final result so do this step with care Start the segmentation algorithm by the pushbutton Go few iterations The smoothness of the final segmentation result can be adjusted by changing the algorithms penalty for curvature This is done by the Curvature slider Note that you can also smooth the segmentation result This is described in detail in Section 15 6 The slider Radius control how large volume is used for cur vature calculation The slider Gradient control how sensitive to boundaries in th
56. TS 28 3 Export contour to clipboard This function ask what contours to export and export the internal repre sentation to the clipboard You can currently chose to export LV endo epicardium RV endo and epicardium respectively 28 4 Export volume of contours per slice This function export the volume of each contour per slice Data is exported for all contours and all time frames If you instead want to have the area per slice you can divide the result with the slice thickness in cm to get the area in cm 28 5 Export image Using this option only the current frame without segmentation is exported as a file You need to select file format and the following formats are sup ported jpg bmp png portable network graphics and tiff The recommended image format to use is png 28 6 Export screenshot Using this option the current frame including segmentation is exported as a file The following image formats are supported jpg bmp png portable network graphics and tiff The recommended image format to use is png There is also an option to save the screenshot file to a PACS system When preparing images for publication it is often helpful to change the color of the contours to black white and increase line width to increase visibility This can be done under the preferences menu see Chapter for further details 28 7 Export movies Exporting movies can be done by either using the built in movie recorder in
57. V segmentation is performed in the main interface according to Section 12 3 52 12 3 EDIT THE SEGMENTATION RESULT E segmentaton y TEP A oh en Step 1 Select slices Step 2 SetLV Select all slices with any myocardium Left click to select most basal slice Clickto adjust cross in the center blue right click to select most epicardial apical slice red ofthe LV Step 3 Start segmentation Figure 19 Interface for LV analysis 12 3 Edit the segmentation result Unfortunately the segmentation result is not always as one would desire We have done as much as we possible can to implement and design a segmenta tion algorithm that is robust and accurate but despite that the algorithm do fail in certain cases and especially on the epicardial contour There are many implemented methods to manually edit the segmentation result Different methods are good in different situations I recommend to learn them all and by experience learn in what situations the different types of manual interaction works best If you experience that editing is a cum bersome task then you are probably doing it the wrong way When the segmentation fails completely please check the following items e Double check that you selected the correct Image type MR Gradient echo MR SSFP CT contrast etc when you loaded the data This is very important for the segmentation result Right click in the thumb nail preview
58. abase We recommend that you start by using our example patient database Down load the file Patientdatabase zip from Medviso AB homepage http medviso com download2 The file is quite large 1 4 GB Unpack the file and place the contents in a folder It is recommended to place it in a subfolder where Segment is installed In Segment you need to set the loca tion of the patient database Click on Preferences and click on Advanced System and DICOM Settings A new user interface appears and click on Database Folder select the folder where the file patientdatabase mat re sides 8 5 4 PACS connection Setting up PACS connection and Segment Server usually requires help from your local PACS support and we recommend that contact us to setup a telephone web based video conference to make this process as smooth as possible The Database and PACS connection manual and the Sectra PACS plugin manual is found at Medviso AB homepage 22 8 6 UNINSTALLATION http medviso com products cmr resources The Sectra PACS plugin may require additional Microsoft Visual C components that can be down loaded from Medviso AB homepage http medviso com download2 8 6 Uninstallation Essentially the uninstallation is similar for all versions 8 6 1 Uninstalling for Windows There is currently no uninstallation software available Remove all files in the folder C Program Segment or C Program Files Segment User pref erences are stored
59. and PACS connection Manual The program can read DICOM and also an internal file format The internal file format called mat files has the advantages that one file may contain several image stacks along with object contours and measurements and it is also much faster and easier to load compared to loading DICOM files It is highly recommendable that when an image stack has been loaded from DICOM files to save the image stack s to the internal file format This makes it then much easier to go back and reanalyse datasets if necessary Note also that the internal file format requires much less storage space that the original DICOM files mainly due to cropping of the images and to loss less compression How to browse your DICOM data in the easiest way is described in Section 9 1 6 The file loading dialog box is started from the main menu under File or by clicking on the icon 3 or by pressing Ctr1 0 This brings up the file loader GUI shown in Figure The file loader process the selected directory and its subdirectories to find the number of files in that directory Since this process takes some time this operation is cached and creates a file called folders cache To recreate the cache press When reading from a CD ROM it is recommendable to copy the CD ROM to your hard drive if you will load most of the files on the CD ROM since random file access from CD is very slow and caching is not possible For further details on how to imp
60. and in the middle panel the corresponding phase for these pixels is shown and in the right panel the resulting phase correction is shown You can select model order and clear the phase correction When you are pleased with the phase correction press Apply to proceed The function automatically finds stationary parts in the image by selecting a percentage of the pixels whose standard deviation of the phase over time is smallest The fraction of pixels taken can be controlled by the edit box Percentile The image is divided into four quadrants and the algorithm to find stationary pixels is applied to each quadrant separately This is done to ensure that there are about the same number of pixels from each quadrant Pixels taken as stationary tissue are shown as red dots in the magnitude image The Magnitude slider controls what magnitude the pixels need to have before being labeled as stationary By selecting the mode of operation as Static tissue ROI then ROI s that are labeled Static tissue are taken as stationary areas This is particularly useful when doing phantom experiments since the automated identification of static areas fails in cases with stationary flow The mode of operation Phantom Experiment GE method automatically finds a flow image stacks that have the same scanning parameters this useful 112 23 4 PHASE UNWRAPPING when a static tissue have been scanned in the same position as the patient as recommended by
61. and select Set Image Description to do this 93 CHAPTER 12 SEGMENTATION OF THE LEFT VENTRICLE e Double check that correct slices are selected for the LV segmentation and that a good LV center point is chosen There are several methods to manipulate the segmentation result Each method have different applications where they work better and it is a learn ing process to learn which tool to use in different situation 12 3 1 Undo segmentation To undo the latest segmentation operation select undo from the tools menu or using the undo icon or using the hot key Ctrl Z 12 3 2 Refine segmentation Refine runs the segmentation algorithm a few iterations and thus further refines the segmentation This functionality is chosen by the two icons O and for endocardium and epicardium respectively Note that the optimization is only run for the selected slices 12 3 3 Propagate segmentation An efficient way of handling erroneous slice is to copy the LV segmentation results from an adjacent slice This is especially efficient in the more basal slices The program copies the LV segmentation in selected slices and refines the position of the contours by a few iterations To propagate a segmentation forward in time one time frame press Ctrl F If the endocardial pen is selected then the endocardium is propagated and if the epicardial pen is selected then the epicardium is propagated The hot key Ctrl F also applies to ROT
62. are further described in 5 A 21 6 Grayzone Analysis Two different methods for Gray Zone analysis is provided in Segment The two methods are the Weighted method and the ROI method 21 6 1 Gray Zone analysis by weighted method The menu item Gray Zone Analysis Weighted Method Default enables the user to divide the scar area into core and grayzone based on the scar seg mentation The result is displayed in the image view as colored overlays of 103 CHAPTER 21 VIABILITY ANALYSIS dark red core and dark yellow grayzone pixels The quntitative core and grayzone values are presented in a message box 21 6 2 Gray Zone analysis by ROI method The menu item Gray Zone Analysis ROI Method enables the user to divide the scar area into core and grayzone based on ROI segmentations and a user selected threshold The result is displayed in the image view as colored overlays of dark red core and dark yellow grayzone pixels The Grayzone Analysis GUI displays a histogram of the pixel intensities of the currently segmented scar volume By dragging the red bar the user can change the threshold for what identifies as grayzone intensity values lower than that of the bar and core the remainder The user can also change the threshold for scar segmentation given as number of standard deviations from remote value by clicking the Increase or Decrease buttons After changing either of these thresholds the values are recalculated b
63. arly useful when anonymizing a complete research study 20 3 Clear segmentation from multiple mat files This utility is useful when one want to clear the segmentation from multiple mat files at once One particular example when it is useful is when a second observer should reanalyse all files In such cases copy all files rename them and run this function 20 4 Sort Folder of DICOM files This utility is useful when you a have a large collection of DICOM files that are in a strange order This is often the case from certain Siemens scanners The program will sort them up in folders that are arranged as 93 CHAPTER 20 UTILITIES patientname patientid studydate stydyid and series number Each folder will contain sorted files according to instance number and trigger time The graphical user interface is shown in Figure gt E DICOM utility and image sorter Sa Name Template OUTIM Input Path Browse UsersWisse LundahNDocuments Source trunk Examples Output Path Browse C Users Nisse Lundah Documents Sourceitrunk Examples Settings V Recusively take subdirs Stable DICOM Extension Mode dem ima File Name Take All Files Mode Start pcom taga Close Figure 30 Graphical user interface for the DICOM sorter Start by selecting input and output folders path directories If the checkbox X Recursively take sub dirs is selected then
64. as performed using the freely available software Segmentv2 0 R4790 http segment heiberg se 19 186 41 Support The commercial license of Segment includes technical support by email It also includes simple feature request such as specialized output formats Fur thermore a commercial licensee will be given a significant weight on how a bug report is prioritized Bugs reported by users of commercial license are usually fixed within 1 2 days The support is provided by Medviso AB With this said we encourage all users to come with questions and feedback but we do not guarantee that we will have time to answer your questions 41 1 Submit bug report When submitting a bug report it is very important to describe how to repro duce the bug and to provide the log file for the session In many cases it is also necessary to provide some files that can be used to analyse the problem It may either be mat files or DICOM files when the problem is loading data into Segment To submit a bug report select the function Support Request under the Help Support menu This will open the graphical user interface where you can describe the bug and attach log files and data such as mat files or DICOM files When all information is entered you press the Send support request and the description entered and the attached files are submitted to Medviso By changing the type you can also submit general questions or enhancement requests H
65. at can be accessed by selecting Open Folder with Log Files from the Help menu It is possible to customize a set of default preferences for every new user of a Segment installation by copying the preferences file to the Segment main folder and renaming it default_preferences mat This preferences file will then be copied to the preferences path of every user that does not 21 CHAPTER 8 INSTALLING AND UNINSTALLING already have preferences saved Further details on how one customizes Segment is given in Customization Chapter in Segment Reference Manual 8 5 2 Setting window positions The position of the main window for Segment can be set by dragging the window to an optional position and size The size and position will be saved so that next time Segment is launched the same position will be used The window position can also be saved for the file loader patient database mod ule PACS connection module general segmentation module fusion module SPECT module and strain module This feature is under development and eventually it will be possible to set the position for all windows until then windows will pop up as an overlay in the middle of the window from which it was launched or in the middle of the main Segment window In case where one have switched to another monitor Segment may move outside the screen In this case you could press Shift Ctrl R to reset GUI positions This is also available under the File menu 8 5 3 Patient dat
66. at one usually would call y axis and for a short axis image stack this would usually be frontal dorsal and Flip y corresponds to left right Note that to preserve a right hand coordinate system it is not pos sible to flip in one image direction alone Therefore a flip in x directions also flips in the z direction The simple flip s above is possible to do when there is an existing segmentation If you require to make rotations flip between two axis you must not have an existing segmentation Flip x amp y transposes the image Flip x amp z switch between basal apical to up down direction and Flip z amp t change between time frames and slices The later option is very useful when loading non standard images This option does not update coor dinate axes so this might be dangerous to use if combining with non flipped image stacks If you need to rotate image volume and maintain correct voxel dimensions please use the multiplanar reconstruction MPR functionality described in Chapter 30 Note that currently the option to rotate 90 degrees right is not working properly 17 8 Resample image stack There are different methods to resample the original image stack 17 8 1 Reformat multiplanar reconstruction This option invokes the multiple planar reconstruction tool described in Chapter 17 8 2 Upsample downsample image By using this option it is possible to upsample or downsample the image stack Note that resampling is only done in the
67. ate Image Stack Show only ROIs Show only myocardium Export Show full image Figure 48 GUI for quantification of T2 T2 values The top left image panel shows the magnitude images for the different echo times adjustable with the echo time slider The right image panel shows the pixelwise T2 values 138 31 2 IMPLEMENTATION The right lower panel shows the fittig curve over time The mean T2 value is presented in the graph and the associated graph title The region for the mean value calculation is according to the selection of the checkboxes to the right either T2 ROI fit or T2 pixel fit The T2 pixel fit takes the T2 values according to the blue cross in the right image panel T2 values can be exported to spreadsheet by using the Export button To create the T2 image stack in the main GUI of Segment use the Create Image Stacks button 31 2 Implementation The detailed implementation of the T2 T2 calculation in given in Chap ter 44 In short the calculation is performed with standard exponential curve fitting that is calculated in the least square sense 31 3 Validation The module has been validated comparing to the open source software MRmap 13 More validation details is available in a separate report from Medviso AB 139 32 SPECT Analysis Module The functions described in this chapter is in US only for off label use and for investigational use The S
68. automatically refine the endocardium The fourth tool puts endocardial pins that guides the automated segmentation The fifth tool is to interactively drag the endo cardium with the mouse 42 10 10 TOOL PALETTE 8 e 98 Lw ENDO EPI INN A pl amp ij ojn Figure 12 Left ventricular toolpalette On the second row is the same as the first row except that the tools applies to the epicardial contour instead of the endocardial contour On the third row from left to right The first icon automatically seg ments both endocardium and epicardium of the left ventricle You need to ensure that the center is in the middle of the ventricle and that all slices that covers the left ventricle are selected see Chaptel12 The second icon X automatically segments the endocardium in the selected slices The third icon X automatically segments the epicardium of the selected slices The fourth icon attempts to remove the papillary muscles This can be use multiple times to successfully remove them The last icon Y deletes the segmentation in the selected slices Generally the space key can be used to toggle between the endo and epicar dial tool counterparts 10 10 2 Right ventricle tools The right ventricle tool palette is shown in Figure The icon is used to click out points in the interpolated contour tool for the right ventricle endocardium and is used for the epicardium respectively The icon amp
69. button down and move the mouse to end point It is possible to interactively drag and refine measurements later The icon is used to crop the current image stack The icon M is used to automatically crop all image stacks to focus on the heart in order for it to work properly at least one time resolved short axis image stack is required The icons 5 and 99 are used to rotate the image stack in 3D space The icon A allows you to find positions in 3D space for all visible image stacks 10 10 5 ROI tool mode The toolpalette for region of interest analysis ROI is shown in Figure The first tool 2 is used to manually delineate region of interests The icon O is used to automatically outline a vessel from scratch Before using this place the center point in the middle of the vessel The icon refines a vessel This is done in all time frames if the checkbox X Single Frame mode is unchecked The icon copies the ROI contour to next time frame and refines it The icon tracks a ROI over the entire cardiac cycle The icon BA selects current color to use to draw ROI s The icon ABC is used to name the current ROI 45 CHAPTER 10 PROGRAM OVERVIEW Bolan CEO Figure 16 Region of interest mode toolpalette 10 11 View tool mode This mode is useful for quickly picking different views of the image stacks The toolpalette is shown in Figure 17 Ai Figure 17 View mode toolpalette The first icon Ll shows
70. classified scar pixels The optimal threshold value is then defined as the threshold corresponding to the minimal number of missclassified pixels 44 12 T2 T2 calculation implementation The signal intensity S in the images can be described with an exponential fit according to S K x el FTE 9 198 44 12 T2 T2 CALCULATION IMPLEMENTATION where R is 1 T2 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 1 Ra Pek 10 where S is the signal intensity of the pixel R is 1 T2 Tp 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 R In the litterature there are some evidence that a constant is advantageous in the fitting process 28 This constant will be implemented in later versions of the module 44 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 44 12 2 Smoothing The smoothing process
71. d 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
72. d manually deleted 99 CHAPTER 21 VIABILITY ANALYSIS Figure 31 Example of scar delineation in the weighted mode The yellow line denotes the complete affected area and the pink line a graphical repre sentation of the corresponding weighted area 100 21 1 AUTOMATIC MODE WEIGHTED SCJ OR FWHM areas in blue The tool amp is used to manually draw regions of microvascular obstruction Microvascular obstruction is indicated in red User interaction and microvascular obstruction can be showed hided by clicking the key o Note when using the weighted method regions with microvascular ob struction needs to be manually drawn if not automatically detected since otherwise they are weighted incorrectly It is also possible to remove re gions with microvascular obstruction with the toggable menu option Remove microvascular obstruction Apex post processing is a technique described in to handle case where the complete slice is infarcted This functionality should normally be enabled The following modes of scar delineations is available e None No viability this will remove viability delineations e Manual mode Manual drawing of hyper enhanced regions e Automated Method Weighted default Automatic scar delineation as described in 4 e Automated Method SCJ method Automatic scar delineation as de scribed in 5 e FWHM Automatic scar delineation using a full width at half maximum method as described in 6
73. e fourth tool is used to plot the phase of the current pixel over time This is mainly useful for debugging purposes It is possible to zoom the image by usage of the zoom icons Y Undo last operation is done by pressing Ctrl Z or the icon 113 CHAPTER 23 FLOW ANALYSIS Velocity original VENC n N i 1 1 4 4 200 400 600 800 1000 1200 1400 1600 Time ms ki gt Tmeframe 6 80 103 ms i Jump size l 2VENC defaut 1VENC iz aesa Instructions Use w a s d or mouse to choose a pixel Up down Slice selection Leftright Timestep selection Shift wrap pixel up control wrap pixel down Space play current slice Figure 38 Example of the graphical user interface for phase unwrapping The left image panel shows the original phase and the right image panel shows the unwrapped phase The long slider adjusts the current time frame 114 23 5 CREATING ANGIO AND VELOCITY MAGNITUDE IMAGES 23 5 Creating angio and velocity magnitude images It is possible to create a so called angio image that is the magnitude image times the velocity magnitude This is available under the Flow menu and Create Angio If you have more than one velocity encoding direction it is possible to create a velocity magnitude image that is the square root of the sum of squares of all velocity directions velocity magnitude 23 6 Coupling magnitude and flow images If
74. e RV center straight to the left of the LV center This estimation can then be corrected manually in the interface shown in Figure The RV center definition is performed as one step in the quantification of myocardium at risk In the interface use the button Set manually to correct the RV center definition and the button Confirm when the RV center definition is sattisfying Use the right mouse click to set the RV center point Figure 52 The interface for definition of the right ventricular center point 32 3 2 Set preferences The MaR preferences are set by the function Set MaR preferences under the Myocardium at Risk and SPECT menu The preferences are set for each image stack which make it possibly to have different preferences for different image stacks The MaR preferences interface is shown in Figure The choice made in the upper panel determine the region for which the count calculations are done in The two selections are ROI the default value and Image The Image selection include all pixels in the image in the defect calculation while 145 CHAPTER 32 SPECT ANALYSIS MODULE the ROI selection only include the pixels within the LV segmentation in the calculations The Count Maximum number is defining the percentile the default value is 100 The Threshold number is determined the percent of Count Maximum which defined a defect the default value is 55 All pixels with a count lower
75. e can use the third format 16 1 1 Save both image stacks and segmentation to one file This function saves both the image stacks and the segmentation to one file This is the recommended way to save the images 16 1 2 Save both image stacks and segmentation as Same as above but asks for a filename 16 1 3 Save only segmentation To save the segmentation results including the measurements of mass dis tance measurements viability and volumes etc select the function Save Segmentation under the File menu hot key is Ctr1 S Then the program asks for a filename The file extension should always be set to seg Note 71 CHAPTER 16 SAVE AND LOAD SEGMENTATION that the segmentation file also contains scar delineations roi s for flow anal ysis etc When comparing segmentation results for different observers it is usually better to store them as separate image files with segmentation Note this function only saves the segmentation not the images This function is kept for backwards compability and may be dropped in future versions of Segment 16 1 4 Save as DICOM To save as DICOM file select Special save in the File menu Then select Save as Dicom You will be prompted for location and filename Note that the file is saved as a DICOM file but essentially it is an internal file format with a DICOM wrapper It can not be used to load and study segmentations with other DICOM compliant softwares 16 2 Load segmentation To
76. e description settings Correctly defined image description parameters is important in the use of automatic analysis tools The image description is divided into three param eters Imaging technique Image type and Image view plane The definition of image description parameters is controlled by manually change the parse file imagedescption tex according to Figure This make it possible to ad just the definition of image description parameters to different acquisition parameters settings There are no limitations in the number of specifications below each image description parameter An example of a parse file is shown in Figure If you have questions please contact support medviso com for further details 29 2 Advanced and DICOM Settings The graphical interface for advanced settings is shown in Figure The GUI is divided into four sections Database settings Segment Server set tings Sending DICOM files and DICOM interpretation 131 CHAPTER 29 CUSTOMIZING SEGMENT Image type General Perfusion Rest rest Perfusion Rest REST Late enhancement DE Late enhancement viabilitermad Late enhancement 3D via cine sbFE Tsempty Ser no Flow Cine m2D Image view plane ge RON ERBEN 2CH 2ch ral 3CH sch 4CH Ach sagittal sag coronal cor Frontal front Transversal trans famaging te Fre unspecified MRSSFP SSFP MASSFP tf2d MRSSFP fiesta MRDE
77. e image the algorithm will be Large value means the algorithm is more likely to stop expanding at boundaries If thecontour of the object expands as planned then continue with Go medium or Go many if necessary 15 3 Manual interaction You can manually edit the result by using the drawing tool or the removal tool 4 For each voxel in the image volume manual corrections can be of three kinds no change i e no manual correction or pixel included or pixel removed By using the tool LI it is possible to draw a box in any of the three orthogonal views This box can then be filled so that it is avoided in the delineation or included in the delineation This is very useful when one want to manually exclude large portions of the image stack from the segmen tation Interactions to edit the segmentation can also be done with region growing 15 4 Region growing Region growing is a tool for doing a new segmentation and or automatically interact with existing segmentation by only placing one inclusion and or ex clusion point The result from the segmentation is shown in the same way as the manual interaction and can therefore remove and add to an exisiting segmentation If no segmentation exists this tool creates a new segmentation 65 CHAPTER 15 SEGMENTATION OF GENERAL OBJECTS 15 4 1 Algorithm The algorithm is based on a level set segmentation but the expansion speed is automatically calculated from the i
78. e marching cubes algorithm and to create a smoother result smoothing of the object representation can be performed The slider Smooth controls the radius of a smoothing filter The value is the number of mm to the 30 signal intensity drop of the filter You need to experiment with the filter setting to achieve proper smoothing For undo history and storing objects only a binary representation is used due to memory consid erations In the Segmentation menu there is an option to create a plot of the smoothing filter 15 7 Viewing final result By pressing the pushbutton Plot 3D the 3D image is plotted in a separate window that can be easily rotated and zoomed There are two checkboxes that controls the view of the isosurface X Plot polygons determines whether polygons are plotted or not X Reduce patch determines whether the number of polygons should be removed by 80 15 8 Tools In the Tools menu it is possible to import segmentation from ROP s contours myocardium or scar data It is also possible to export the segmentation into 67 CHAPTER 15 SEGMENTATION OF GENERAL OBJECTS STL files that can be loaded into 3D modelling softwares or rapid prototyping softwares In the STL export a polygon mesh is created as a isosurface of the from the level set function It is recommended to smooth the model prior to the STL export 15 9 Prototype based segmentation The prototype based segmentation is a newl
79. e when you have images on a CD structured or not that you want to copy to your harddrive and subsequent analyze This function assumes that you have set the location of your CD drive in the preferences see Chapter 29 This function sorts and name the files in the same manner as the sorting utility DICOM cache and thumbnails are also created 20 6 Create DICOM cache for folders recursively This function ask for a folder and creates DICOM cache files for all subdi rectories This functionality is highly useful when you have copied large sets of DICOM files to your local harddrive that you need to load into Segment It takes a long time to run so a good idea is to start this function over lunch Once this is done loading of your DICOM files will go much faster 20 7 Create thumbnails preview recursively Analog to creating of DICOM cache files but creates thumbnail preview for all subdirectories Depending on the number of subfolders this function may also take quite long time to run 20 8 Find patient details in mat files This utlity allows to scan your entire harddrive or network drive for patient details in mat files Output is a list of all patients occuring in the directory tree This feature is useful when you want to ensure that you have not stored any sensitive information on your local computer laptop for instance The output is an Excel file where each row mat file with patient information 95 CHAPTER 20 UTILITIES
80. ed phase information of static tissue in the chest wall to function properly The graphical user interface for compensating for eddy current effects is shown in Figure 110 23 3 COMPENSATING FOR EDDY CURRENT EFFECTS Figure 35 Example of plotting of velocity over time The error bars shown the standard deviation of the pixels within the ROI over time 3D velocity profile Aortic ascending flow File Edit View Insert Tools Desktop Window Help DSHS hea S08 a0 Wik sa better D A Figure 36 Example of plotting of a 3D profile of the velocity distribution 111 CHAPTER 23 FLOW ANALYSIS Correction for eddy current effects DER Preview of static map Phase of static pixels cm s Estimated phase error cm s Applied phasecorrection cm s Magnitude threshole First order polynomial Linear a gt gt Second order polynomial Quadratic Kal Static tissue ROI Phantom Experiment GE method Percentiles 10 S l AAA Time dependent eddy currents not defaut cancel clear cacume J Aey Done Figure 37 Example graphical user interface for compensating of concomitant field effects In the left the identified static tissue is the displayed
81. egment We strongly recommend using SSD disk for reading data 15 8 Installing and Uninstalling The descriptions for first time installation is divided into two main sections describing Windows standalone installation section 8 1 and source code in stallation section 8 2 respectively The sections after that describes general settings that should be performed regardless of installation type 8 1 Installation of Standalone version for Windows This section is written for first time installation of Segment For upgrading see the Section 8 4 The program is written in Matlab in order to run it you therefore need to install Matlab Compiler Runtime first Note that to be able to perform these steps below you need to have administrator privileges on the machine If you are using Windows Vista then please also refer to Section 8 1 4 8 1 1 Installing Matlab Compiler Runtime If you have Matlab and Matlab Compiler Runtime MCR installed on your computer this step may not be necessary provided that you have exactly the same version as used for compiling Segment Currently Matlab Compiler Runtime R2014a is required Download the file MCR_R2014a_win64_installer exe Exact name of the file depends on operating system you are installing to Download the file to a suitable location i e your desktop or a temporary folder and double click it Follow the instructions in Figures This step to install MCR Installer does only need to be perf
82. en written by Helen Soneson as her Master thesis work 14 and resides on the work by Erik Bergvall for strain calculations and myocardial tracking 15 This module is not available yet to researchers since it is under development and will be released as soon as the underlying method is properly published Preliminary results about the method was presented at SCMR 2008 16 17 Strain calculations require velocity encoded MR images with two velocity components An example of such an image stack are shown in Figure The leftmost panel is the magnitude image stack the two rightmost are the velocity image stacks Figure 57 Example of a velocity encoded magnitude image stack and two directional velocity encoded image stacks Before starting strain calculation the myocardium of the left ventricle need to be manually outlined in end diastole One method to do this is to use the endocardium tool 2 directly in the velocity encoded image stack One tip before outline the myocardium in a long axis image is to first set the 155 CHAPTER 34 STRAIN ANALYSIS MODULE Number of points along the contour in Preferences under the Preferences menu to 300 This make it easier to do small changes in the segmentation The other method is to segment the myocardium in the anatomical balanced or SSFP image stack and then exported it to the velocity encoded image stack The exportation is done with the function Import From Cine Stack under the menu S
83. erity of the defect It is presented for the whole LV as well as for each of the three coronary arteries LAD LCx and RCA To be able to calculate the TPD for LAD LCx and RCA the RV center need to be defined This is done as described in the previous section Define RV center 32 4 3 Manual perfusion scoring Segment provides an inferface for manual scoring of tracer uptake and my ocardial infarction The inferface is illustrated in Figure The scoring is performed for each of the segments in the AHA 17 segment model Summed scores are calculated for stress SSS rest SRS and stress rest difference SDS There are two modes for the scoring the first illustrating the rest and the stress ungated images and are for scoring of the tracer uptake The scoring values should be between 0 and 4 as described to the right in the interface The second scoring mode is found by choosing gated under the Visualization mode This opens the interface for scoring the precens of my ocardial infarction For this pupose the rest gated and ungated image stacks are used and the scoring values should be between 0 and 2 as described to the right in the interface 150 32 4 PERFUSION ANALYSIS Stress Segmentation SSS 14 LVM 105 LVM 106 E EDV 110 mi EDV 101 mi 9 show SRS 4 EF 64 Be hide SDS 10 Visualization mode Scoring of tracer uptake ungated 0 normal 1 equivocal gated 2 moderate 3 seve
84. ert colors Invert colors remaps all pixels with the equation sycw 1 Soja where s denotes pixel intensity This functionality is undoable by repeating the operation 76 17 6 SET COLORMAP FOR CURRENT IMAGE STACK 17 5 4 Precompensation This functionality might be useful for gradient echo MR images to minimize inflow artefacts This option scales each time frame such as the mean image intensity is constant over time Note that this function is not undoable 17 5 5 View intensity mapping Brightness and contrast settings are implemented so that the pixel intensity is remaped before being rendered Currently this remaping function is a cropped linear function but will be extended to a sigmoid function in future versions of Segment This functionality plots the current intensity mapping 17 5 6 View true image intensity The function displays the current slice and time frame and a color scale coupled to the original pixel values in the DICOM file 17 6 Set colormap for current image stack This function sets the used colormap for the selected image stack Supported colormaps are shown in Figure Gray Hot HSV Jet SPECT Figure 24 Colormaps 17 7 Flip Rotate image stack By using this function it is possible to swap the direction of one axis For instance if want to flip an image stack upside down apex base use Flip z 77 CHAPTER 17 IMAGE TOOLS Flip x corresponds to wh
85. et us know if this is a desired feature We will need to have some example images since we do not have access to details about this e Timing time increment between frames may not be correctly calcu lated unless for IntraGate scanners Timing information is taken from EchoTime and RepetitionTime please see Section 37 1 7 for details 37 1 Implementation details In this section details on how Segment interprets the Bruker File format is given An overview of the folder tree for a Bruker examination is given in Figure This example examination contains two scans and where the first scan contains two series 170 37 1 IMPLEMENTATION DETAILS 2dseq d3proc reco acqp Subject Figure 66 Example of file folder tree for a Bruker examination In this case the number of scans are two and for scan 1 there are two series Boxes represent folders and plain text without a box represent a file Only the illustrated folders and files are read all other files and folders are ignored 171 CHAPTER 37 NATIVE BRUKER READER MODULE 37 1 1 Read files The following files are read by the Bruker reader module all other files are ignored e subject file This file contains subject data common for the entire exam e acqp file This file contains image acquisition information of the scan e reco file This file contains information for the image serie e d3proc file This file contains additional information for the image
86. f myocardium at risk from myocardial perfusion SPECT in patients with acute coronary occlusion J Nucl Cardiol 17 5 831 40 2010 203 BIBLIOGRAPHY 25 26 28 29 30 204 P Sorensson E Heiberg N Saleh F Bouvier K Caidahl P Tornvall L Ryden J Pernow and H Arheden Assessment of myocardium at risk with contrast enhanced steady state free precession cine cardiovas cular magnetic resonance compared to single photon emission computed tomography J Cardiovasc Magn Reson In press 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 P A Cain M Ugander J Palmer M Carlsson E Heiberg and H Arheden Quantitative polar representation of left ventricular my ocardial perfusion function and viability using SPECT and cardiac mag netic resonance initial results Clin Physiol Funct Imaging 25 4 215 22 2005 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 an
87. for the whole LV as well as for each of the three coronary arteries LAD LCx and RCA To be able to calculate the TPD for LAD LCx and RCA the RV center need to be defined This is done as described in the previous section Define RV center 32 4 2 Automatic quantification of stress perfusion defect When there is only a stress MPS image stack present the perfusion analysis tool Auto Perfusion Analysis under the Perfusion and SPECT menu can only 148 32 4 PERFUSION ANALYSIS LVM 104 g TID 1 03 REST EF 56 26 Defect 8 8 ml TPD 4 TPD LAD 14 TPDLCx 0 TPD RCA 0 STRESS EF 54 Defect 24 24 mi TPD 12 TPD LAD 31 TPDLCx 0 Stress Rest Change TPD RCA 0 STRESS REST CHANGE Defect 17 17 mi TPD 11 TPD LAD 19 TPD LCx 0 TPDRCA 0 Stress Rest Change Figure 55 The perfusion analysis interface The red line is the endocardium the green line the epicardium and the yellow line the perfusion defect 149 CHAPTER 32 SPECT ANALYSIS MODULE quantify stress perfusion defects The automatic quantification is performed by using the counts in the stress image stack and the result is illustrated in an interface similar to the interface shown in Figure The defect quan tification is presented both as percentage extent of the LV absolute volume in ml and by Total perfusion deficit TPD TPD is a measure of the per fusion defect including both the extent and the sev
88. fusion and SPECT menu Figure 54 show the result by the automatic registration algorithm From the inter face it is possibly to manually correct the registration by using the tools to the right in the interface To reset the manual corrections and go back to the automatic registration use the button Reset registration in the interface To continue with the automatic perfusion analysis use the button Perfusion analysis Segmentation and quantification The quantification of stress induced ischemia and infarction is performed by using the function Auto Perfusion Analysis under the Perfusion and SPECT menu A pre request to perform perfusion analysis is image registration 147 CHAPTER 32 SPECT ANALYSIS MODULE Figure 54 The rest stress registration interface between rest and stress image stacks as described in the previous section Figure illustrate the interface for showing the perfusion analysis result The defect quantification is presented for both the rest and the stress study as well as for the stress rest change The rest defect is the quantification of myocardial infarction and the stress rest change is the quantiafication of stress induced ischemia The defect quantifications are presented both as percentage extent of the LV absolute volume in ml and by Total perfusion deficit TPD TPD is a measure of the perfusion defect including both the extent and the severity of the defect It is presented
89. g the region of interest is described in Chapter If you are not satisfied with the ROI there are two methods that can be applied 23 1 1 Refine Refine operation operates on the current time frame or all time frames de pending on the checkbox amp Single frame mode Short key for the refine function is Ctrl R You need to have the ROI pen active when using the hot key Re fine on all time frames is particularly useful if the vessel is fairly round and not to close to other surrounding tissue 23 1 2 Refine and propagate Start at the first time frame of the time series If pleased with the result simply use the right arrow key on the keyboard to proceed to next time frame When you find a time frame where you are not pleased with the segmentation use the ROI pen to adjust the contour or use the refine option Ctrl R with the checkbox amp Single frame mode enabled Continue by propagating the contour by pressing Ctr1 F 23 1 3 Shrink flow ROI If the RIO is outside the vessel then it might be advantageous to shrink the ROI followed by one ore more refine operations Shrink flow ROI is found under the Segmentation menu and the submenu ROI and Flow tools 23 2 Plotting the result of the flow analysis The flow plotting utility is started by using the icon A or by using the function Plot flow curves under the Flow menu An example of the graphical user interface is shown in Figure In the upper right area
90. h multiple stored objects you can perform binary operations on them to merge or combine objects in other ways by using the OR AND NOT You can also rename objects by the using the pushbutton Rename or sort them in the list by the buttons Up or Down The pushbutton Sort sorts the object by decreasing volume If you have many objects it is possible to store them all under different names This is done by the function Label This label function can also be useful to detect if two objects are joined or not The used connectivity is 66 15 6 SMOOTHING OBJECTS 6 connectivety If you have one object that you want to try to split into two objects this can be done by choosing the object in the list and using the function Split The function erodes the object to split it at its weakest point After the object is split into two or more parts the algorithm reconstucts the parts so that the effects of the erosion are removed The new objects are stored into the list 15 6 Smoothing objects The object is internally stored by allocating one byte per voxel If this byte contains a value over 128 then the voxel is inside the object otherwise the voxel is outside the object The algorithm is binary by construction and each voxel is given either the value 255 or 0 The contour of the exported files are created by th
91. havior is to include only the pixels where the center of the pixel lies within the ROI The checkbox X Allow DICOM cache allows creation of cache files for tags in DICOM files to be generated The web browser to be used can be chosen in the drop list by either choosing a program if it is installed in the default location or choose other to browse for the program file to use for example select chrome exe or firefox exe 130 29 1 IMAGE DESCRIPTION SETTINGS Customization of the Report Module is described in Chapter 38 29 1 Image description settings The automatical definition of image description parameters upon loading is controlled by a parse file A schematic view of the parse file is shown in Figure Imaging technique output string matched against sequence name string matched against series description string matched against modality string matched against filename matlab code Image type output string matched against sequence name string matched against series description string matched against modality string matched against filename matlab code Image view plane output string matched against sequence name string matched against series description string matched against modality string matched against filename matlab code Figure 44 Schematic view of the parse file for imag
92. he Export button export strain values to a clipboard These values are only given section wise and the values in each sector corresponds to the mean value of the pixels in the sector The sectors are divided according to American Heart Associations 17 segments model 156 34 1 VELOCITY ENCODED IMAGING Figure 58 Example of the strain GUI 34 1 2 Corrections of the segmentation To make manual corrections in the calculated segmentation select use left mouse click in the image to move contour points Delete manual point by right click on the added point When you are satisfied with the manual correction in all time frames push the Retrack button The Delete button deletes all manual corrections 34 1 3 Strain analysis One method to evaluate the strain calculation is to export the segmentation from the velocity encoded image stack to the SSFP image stack after the strain calculation is done This is done with the button Import From Strain The motion of the myocardium can then be compared to the myocardial movement in the SSFP image stack It should be noticed that the two im ages SSPF and velocity encoded are not acquired during the same heart beat which can result in differences in position of the myocardium With strain calculated in the current velocity encoded image stack it is pos sible to produce a graph over time for strain by the button Graph 157 CHAPTER 34
93. her Go few Go medium or Go many If more iterations is desired it is possible to choose if the startindex from the prototype should be used as startindex should be used or not in the checkbox amp Startindex 69 16 Save and Load Segmentation A key feature in Segment is that all measurements and user interaction can be saved so that is possible to go back and see how the analysis was done Saving and loading works differently in the Clinical mode or in the research mode In the clinical mode then Ctrl S automatically saves to the patient database and in the research mode you will be prompted where to store the file Loading operations in the clinical mode opens the patient database whereas in the research mode it opens the file loader GUI 16 1 Save images Segment is able to save files in three diffrent formats One old and soon to be obsoleted that stores only the image information of one single image stack one that stores all image stack with all segmentation into one single file and one that stores all images stacks with all segmentation into one single file that is also a valid DICOM file The second format is the most stable and is recommended when one observer is reviewing the images and one would like to have the opportunity to go back and check how the analysis where made If one needs to store the file in an enviroment which only accepts DICOM images such as a PACS on
94. hift F You can label and color each ROI individually For flow measurements each ROI can also be assigned with a sign that will be multiplied with the velocities inside the ROI The default sign is positive The following names of ROPs are reserved for various purposes Remote ROI used to implement 2SD from remote as described by B Scar region ROI used to implement 2SD from remote as described by Bl Static tissue used for concomitant field correction described in Chap ter 23 Aortic ascending flow Aortic descending flow Pulmonary artery Vena cava inf Vena cava sup Vena pulmonalis inf Vena pulmonalis sup Vena pulmonalis dex Vena pulmonalis sin Sinus coronarius Lung Heart 18 1 Creating ROI s There are several possibilities to add ROIs Perhaps the most intuitive method is to draw the ROI by using the 2 The ROI will be given the same 81 CHAPTER 18 REGION OF INTEREST ANALYSIS name and color as the latest modified drawn ROI This is very useful if you would like to draw several ROI s of the same kind Start by drawing the first ROI name and color it Thereafter you can continue to draw the remaining ROT It is also possible to add fix sized ROI s by using the Add fix size ROI un der the ROI menu This will add a fix size ROI and you will be prompted to enter the diameter This function applies to the current slice Another approach is to add ROI s in the myocardium between the endocardium and
95. in a messagebox and copied to the clipboard allowing the user to paste them into a spreadsheet 123 28 Export Images and Results There are many options to do batch exporting from multiple mat files Please see Chapter 20 for further details 28 1 Export results to clipboard These functions export results such as LV mass ejection fraction volumes etc to the clipboard Data is outputed in a format so that it directly can be pasted into Microsoft Excel by usage of Ctr1 V in Excel or other spread sheet softwares When you need to export data from multiple files it is strongly recommended to use the utility to summarize mat files described in Section 20 10 28 1 1 Allstacks with header This function exports the results of all image stacks and includes a header line above Segment tries to use the image type to determine which image stacks are short axis cine images which are used for mass and ejection fraction flow image stacks delayed enhancement image stacks and so forth 28 1 2 All stacks Same as above but no header line is included in the output 28 1 3 This stack with header This function only outputs results from the current image stack and includes a header line 28 1 4 This stack Same as above but without including a header line 28 2 Export volume curve to clipboard The volume curve both endocardial volume and epicardial volume is copied into two columns 125 CHAPTER 28 EXPORT IMAGES AND RESUL
96. in plane direction When downsample an appropriate anti alias filter is applied The used interpolation algorithm is bicubic interpolation This functionality is not undoable 17 8 3 Upsample downsample slices The number of slices can be upsample of downsampled This functionality is not undoable 78 17 9 ADD NOISE 17 9 Add noise By using this functionality it is possible to add noise Gaussian white noise to the current image stack The amount of noise is regulated by the std of the noise 17 10 Calculate temporal mean image This function creates a new image stack that is the temporal mean of the current image stack 17 11 Set current frame as first frame This function shifts the time series cyclic shift such as the current time frame becomes the first time frame in the time series Note that it only applies to selected slices 17 12 View K space This menu option shows the k space for the current frame and slice 17 13 Set image description By using this menu option the image type image view plane and imaging technique is displayed and a menu is shown where new image descriptions can be selected Image type and image view plane is used by Segment to find what image stacks to take measurements from This applies to the utility to summarize multiple mat files and the report sheet generator Imaging technique is used to find segmentation parameters and are therefore critical for a good automated segmentation For fu
97. in the Application Data and the subfolder Segment under each user account Windows To uninstall the Matlab Compiler Runtime use the Windows functionality Install or Remove Programs in the control panel menu 8 6 2 Uninstallation for source code The uninstallation for the source code version is trivial simply delete all Segment related files 8 7 Trouble shooting The absolutely most common problem is the failure to not login as a local ad ministrator of the computer The second most common mistake is not to read the installation instruction provided in this user manual or on the homepage To trouble shoot the installation you can see if the Segment installation program actually was successfully started by checking for the existence of log files Segment creates a log file during installation this file is stored in the user folder i e Documents and Settings Username and Application Data and the subfolder Segment Note that this folder by default is hid den If you have problems installing Segment please send this log file to support medviso com together with a description on what problems where encountered 23 9 Loading Image Stacks The best method to load and manage studies is by using the Patient Database Module described in Segment Database Manual For clinical use we dis curage the direct use of the DICOM loader since this is a sub optimal work flow in the clinical situation instead please look at the Segment Database
98. in the LV myocardium is pre sented by using Plot 3D Surface under the SPECT menu This will open a separate graphical user interface shown in Figure 32 2 Automatic segmentation of the left ventricle The function Auto Delineate LV under the SPECT menu automatically seg ment the left ventricle in the current image stack To use the function the 141 CHAPTER 32 SPECT ANALYSIS MODULE Stress gated Rest gated Apical SA Segmentation LVM 105 g LYM 106 g EDV 110 ml EDV 101 mi show EF 64 EF 68 ae Visualization mode ungated fated Gated E tes Prev Stop rm 120 10 ee Frame rate E 4 tt bw sone a Normalize counts aa each time frame ee ane 4 over cardiac cycle ee Correct LV segmentation Correct LV segmentation E ia E mm More apical mal Moea E Figure 49 Graphical user interface of the 2 dimensional visualization for SPECT images BDisurface Mean radial counts Figure 50 Graphical user interface of the 3 dimensional visualization for SPECT images 142 32 2 AUTOMATIC SEGMENTATION OF THE LEFT VENTRICLE image stack must fulfill the following requirements e The image stack need to be in short axis projection e The Number of points along the contour must be greater then or equal to 50 define in the Preferences menu e The slices have to be in the order basal to apex when go thro
99. ind 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 200 Bibliography 1 J Sjogren J Renner H Arheden and E Heiberg Prototype based image segmentation A novel method to incorporate a priori information in a level set method In SSBA08 Lund 2008 B Nilsson and A Heyden A fast algorithm for level set like active contours Pattern Recognition Letters 24 9 10 1331 1337 2003 R J Kim E L Chen J A Lima and R M Judd Myocardial Gd DTPA kinetics determine MRI contrast enhancement and reflect the extent and severity of myocardial injury after acute reperfused infarc tion Circulation 94 12 3318 26 1996 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 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 L
100. ing functionality 46 49 RA e 49 11 2 Image description upon loading 49 51 OE Be as Se e 51 YE E VIE Dee 51 1212 Mitral annulusl coslada 51 E O RAS 51 12 3 Edit the segmentation result 53 oa es e 54 pa prees a E RR A ee 54 cada a BOBS 54 ENE 54 55 CEEE 55 EREET ON 55 nee whe A 55 ee 56 12 3 10 Removing segmentation result 2 2 2 2 56 57 59 14 1 Click an image to show point location in all views 59 ill CONTENTS 61 RT une ee ee 61 a A eh er re ee ee 63 e a N E A Ge 63 15 2 2 Optimizing expansion speed 63 15 2 3 Start the segmentation tool 64 DR Eee Bak Pom ack o Bee 65 15 4 Region growing soo meo ser ewe cor 4 65 de AR arta arg BAe Be 66 15 4 2 Start the segmentation tool 66 yaaa bee ke bee ek NS 66 lc sgt Sek D g a ene A he 67 15 7 Viewing final result 2 73 4 46444 a se es 67 158 Tools wu 5 ve Rk ee See aa ee wre a 67 me Bee eee ee 68 16 Save and Load Segmentation 71 16 1 Save images a a re ea 71 on en 71 a E AA oe Ge 71 Lied didas 72 sa Bea A A 72 16 3 Importing segmentation result 72 E AE 12 75 17 1 Crop image stackle 2 24 ze a aaa fa aaa Ce oe ee oe es 75 seee ee ie 75 17 2 Remove time irames osc wa a Ewa es e ss vr 75 17 3 Remove slices 3 0 6 4 4 00 u 4 ke eu Hee en alba eo o 75 ee ee re 76 17 5 Manipulate light contrast os oms se sr lt
101. ints to remember 1 Even though the submitted files are encrypted your files should be anonymized Anonymization of mat files are available under either Image Tools menu or the Utilities menu Anonymization of DICOM files are available under the Utilities menu 2 Additional files to submit should be placed in a folder and the folder is then submitted 187 CHAPTER 41 SUPPORT 3 Remember to name your files wisely otherwise we will not be able to identify which file belongs to which support request 4 Remember to mention the filename uploaded in your support ques tion request 41 2 Data privacy policy Medviso AB will strictly keep the data safe and not distribute it and any data or information from it such as possible pulse programming ideas post processing ideas etc etc Medviso will not utilize it for other purposes than debugging purposes or to answer the specific questions unless other is agreed upon When the support case has been closed then the data will be deleted If you have questions please contact support medviso com for further details 41 3 General support issues To get into contact with developers at Medviso AB send email to support medviso com 188 42 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 communit
102. is software for investigational purposes 2 License Terms The software can be used under three different license forms More detailed information and pricing of the different license forms is given on Medviso AB homepage http www medviso com 2 1 Free or charge for non commercial research The software is free to use for non commercial research or educational pur poses if and only if you reference it properly and send full bibliographic information such as Pubmed link of your final work when published or ac cepted for publication Details on how to reference the software are given in Chapter You may not use the software for clinical routine or commercial applications such as company paid pharmaceutical trials without contacting the author Details about commercial clinical use is given below Note that the software is copyright and may not be redistributed resold without permission of the author 2 2 Commercial or Clinical use To use the software for clinical routine or commercial research see above you need a commercial license of Segment Details on how to acquire a such license are found on the homepage http www medviso com This version of Segment is FDA 510 k approved K090833 The license includes some extended functionality in forms of different modules that are not available in the free research only version Depeding on the exact configuration your commercial version may include some or all of the following extra featu
103. is done by normalized averaging where the certainty of each pixel is taken into acount to avoid the effect of uncertain pixels 29 The smoothing kernel is a Gaussian smoothing kernel illustrated in Fig ure The certainty is calculated linearly as a function of the error measure calcu lated in Section 44 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 30 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 11 199 CHAPTER 44 IMPLEMENTATION DETAILS Figure 69 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 69 and M is a temporary map used to calculate the final smoothed T2 T2 value as T M C F 12 where T is the smoothed T2 T2 value M is the map calculated in Equation 11 denotes pixel wise division C is the certainty map denotes convolution and F is the smoothing filter kernel 44 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 k
104. izing Segment This chapter describes how to customize Segment It is recommended to set the preferences of which folders to use to avoid browsing each time you want to load or save a file The GUI for setting preferences is shown in Figure 43 It is invoked by using the menu Preferences on the main menu Default folder locations Set Data Path C Users Nisse LundahNDocuments Source trunk export Patn copy CAUsersinisse LundantDocuments Sourcettrunk CD Path F Drawing Viewing E Add pins when adjusting contour E Black White view Line width for delineations Marker size for endo epicardium Distance to contour for adjustment Number of points along contour Analysis 9 Radial profiles from endocardial centroid Radial profiles from epicardial centroid default Modified centerline method 80 Number of radial profiles to evaluate Include touched pixels in ROI not default El Use Light Contrast System V Hide files starting with on Unix Allow DICOM Cache Show description instead of folder name Unsafe Mode Do not ask V Use fast load of filename preview 7 Check for new version on startup Web browser to use Number of interpolation points Y Exclude Papillaries Internet Explorer Number of visible thumbnails Advanced System and DICOM settings Blind Subject Identity Deven eet San ee See 7 Single slice interpolated for gray scale PACS settings a od
105. k This time frame will be the initial time frame for the strain tracking 4 Start the strain module by selecting Strain Analysis under menu Strain From Tagging in the main menu The Strain interface is shown Figure 158 34 2 TAGGING IMAGING el u ul Crop tagging image stack Crop as close as possible around the LV in order to improve the strain tracking and speed up the strain calculation time Default auto crop a Cancel Figure 59 Strain cropping interface 159 CHAPTER 34 STRAIN ANALYSIS MODULE E Myocardial Strain lt elos Anatomic Image Tagging Image 600 Time ms 800 Peak circumferential strain u gt Hide Points agging Image T Y LV Rotation f Oms Hide Fr Previous Play l Next ch Figure 60 Strain analysis GUI 5 Define LV rotation by setting the white line in the middle of the RV lumen using the slider and press Analyse to run the myocardial strain quantification 6 Verify the strain tracking by using the movie tools 7 Strain over time and peak strain is shown in the figures to the right according to the selected parameters 8 If needed manual correction can be performed by using the Move Contour arrows or moving the LV segmentation interpolation points in the initial time frame in the tagging image stack Then run the strain quantificati
106. k 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 BetweenSlices 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 44 4 VOLUME CALCULATIONS e Velocity encoding VENC in cm s For non velocity encoded images this should be 0 How this is interpretated involvs proprietry informa tion of different
107. le is used for performing analysis of perfusion image stacks Quotes between maximum upslopes of rest and stress images can be calculated for each sector of the myocardium 36 1 Module overview Before opening the perfusion analysis GUI make sure to have one open im age stack whose image type is set to Perfusion Rest and one whose image type is set to Perfusion Stress An overview of the perfusion analysis GUI as it appears when launched is shown in Figure 63 From left to right each im age column contains Stress Rest Cine and LGE images respectively Image slices are shown with the most basal at the top and the most apical at the bottom If the perfusion stacks contain more than three slices a scrollbar al lows the user to toggle between them Segmentation contours are shown but can be disabled by unchecking the X Contour box The X Rotate checkbox is used to set images in rotation mode This causes the images to zoom in on the contour and displays the borders for myocardial sectors as well as a horizontal yellow line from the center to the left of each image By dragging this yellow line the user can rotate the images to align them properly with the sector partition When the mouse button is released the line will rotate back to its original leftward position and drag the image with it The timebars below the Stress Rest and Cine images enable the user to step in time The Stress and Rest timebars each ha
108. ls in the file format used in the Bruker Module is given in Section 37 1 The reader is available under the File menu The file loader GUI is shown in Figure The first step is to select the subject file This file is usually called just subject or subject txt Then all available subject info is shown in the top left panel A list of available studies are shown in the lower left panel When selecting on study the image series usually only one are displayed The Load will load the selected studies series To load many studies into one image stack just select more studies in the lower left panel Note that when loading many studies into one image stack each study needs to contain only one image serie The button Dismiss will close the file loader The button Clear will clear the current subject to allow you to select another subject The following limitations apply to the Bruker reader e The reader is still experimental and all paravision features may not be implemented If you are experience problems with the Bruker reader please report them to support medviso com 169 CHAPTER 37 NATIVE BRUKER READER MODULE Select subject file Info Name TAC Figure 65 File GUI for loading bruker images e The reader does currently not read 3D coordinates and thus the plane intersection features in Segment will not work e The reader does not read phase contrast images Please l
109. lter button it is possible to plot the filter in the temporal domain Cur rently the filter is applied directly to the ROI curve Finally the Export button exports all parameters to the clipboard The Max Min Export button exports the values and timing of min max min max slopes and FWHM Note that that when changing plotting options the plot is not updated until you click Update 18 6 ROI histogram This function plots the histogram of ROI s When initiated the program asks for a selection criteria on what ROI s to include If no ROI s are present then the histogram for the whole image current slice and time frame is displayed The most common percentiles are also calculated and exported to clipboard An example is shown in Figure 18 7 Multiple threshold analysis This function calculates the number of pixels inside the ROI s above the se lected threshold Before starting the program prompts for start threshold end threshold and number of levels All curves are plotted at the same level The offset of each curve is displayed All numeric data are copied to clip board There is also a visual mode where the pixels above a certain threshold are color coded An example of the visual analysis is shown in Figure You are also prompted whether to use the internal normalized image pixel values or the original data from the file The non normalized range can be found b
110. magnitude and flow image stacks have been loaded into Segmentwithout being coupled to each other it is possible to couple them using the Couple Magnitude Phase Flow Image Stacks from the Flow menu Available magni tude and phase image stacks are then identified and coupled using heuristics 115 24 Pulse Wave Velocity Analysis The functions described in this chapter is in US only for off label use and for investigational use An overview of the Pulse Wave Velocity module is shown in Figure Upon launch the module automatically finds the image stack that contains a measurement labelled Aortic Length and the two flow image stacks that contain ROT s labelled Aortic ascending flow and Abdominal aorta The image on the left of the GUI shows the image containing the measurement This measurement is displayed in yellow and the intersections with images con taining flow are displayed as white lines The plot on the right side shows the flow curves of the Aortic ascending flow ROI in blue and the Abdominal Aorta in red For each flow curve the tangent of the upslope is calculated using a Gaussian smoothing function and displayed as a dashed line in the corresponding color The sigma parameter of the smoothing function can be adjusted using the slider on the right of the plot Pulse wave velocity is calculated using the length of the Aortic Length measurement and the time between the upslopes of the flow curves The time is measured as the temp
111. malized with BSA 38 1 3 Headings for textual report There is also a large textbox where it is possible to enter free text comments on the study This text is then stored together with the segmentation A few formatting tricks can be used in this box e To divide the text into paragraphs enter a blank line between the text blocks to be used as paragraphs e To start a paragraph with a headline in bold print simply begin the paragraph with the text to be used as headline then insert a new line where the text body is entered 177 CHAPTER 38 REPORT MODULE e To insert a super headline do the same as above except that the text is entered in all upper case letters A super headline may be followed by a regular headline For simplification standard text templates are supplied by Medviso AB An example of such a template is the following PATIENT HISTORY lt Enter text here gt GENERAL IMPRESSION LV function lt Enter text here gt RV function lt Enter text here gt FINAL COMMENTS lt Enter text here gt 38 1 4 Reviewing doctor The final textbox in the GUI allows for including the name of the doctor performing the analysis and generating the report If entered the name of the doctor appears by the logo image at the beginning and by the signature field at the end of the report 178 38 1 CONFIGURATION MEDVISO Report generated 2011 03 15 by Dr Gonzalez Reference values from Maceira Males Age 30 39
112. mote It is possible to do scar delineation as proposed by Kim et al where the infarct is determined as pixels with an image intensity that is higher than the mean plus two standard deviations from the mean in a non infarcted remote region In the original method by Kim et al when one read the paper carefully they used two types of ROI s both remote ROI s and also a scar region ROI in which the thresholding was applied Therefore the same ap proach is also applied in Segment To draw remote region use the ROI drawing tool 2 or Add RO s in sector under the ROI menu The latter option adds ROI s in a sector in selected slices with a position specified as an angle the width as and angle and finally the distance from the endo and epicardium as percentage of the wall thickness This option automatically flags the ROI s to be remote regions but if you use the ROI drawing tool i you need to manually flag that by right clicking on the ROI and select Select ROI label on the pop up menu When drawing a subsequent ROI the label of the ROI is copied from the last modified ROI so you only need to first draw one ROI then label it and draw all remaining ROI s If you do not draw a remote region in the threshold for that slice is then intra extrapolated from adjacent slices Using the default viability options this approach will only set a threshold to the level set algorithm based on the drawn ROPs To draw the scar region ROI s Scar region ROI
113. n or how you do it or what PACS you are using outputs files in a completely unstructured way all patients and all time frames and all slices are mixed into the same folder In Segment there is a sorting utility that can be accessed on the main menu that can sort the files This is described in Chapter 9 2 Matlab format details Internal format used by the program The image needs the be stored in the variable im or setstruct and must be in single precision format The dimensions must be x y t z If you do not have time resolved data make sure to make the temporal dimension singleton i e always put in a 4D array It is possible to also give dimensions and patient specific information as well as a preview image To learn about this load an image stack from DICOM 31 CHAPTER 9 LOADING IMAGE STACKS images and select Save Both Image Stacks and Segmentation As under the File menu Then load the file in Matlab and study the variables in the file Details about the file format is given in the Segment Technical Manual 32 10 Program Overview This chapter provides an overview of the program Another good method to get an overview of the program is to read the example in Chapter Yet a good method is to view the on line video tutorials The tutorials are available under the Help menu An example of the main graphical user interface is shown in Figure 8 The major portion of the user interface is occupied by a viewing area whe
114. n be added by left mouse click in at the position where you like to add the point 12 3 6 Manually drawing the contour This functionality is chosen by the two icons and for endocardium and epicardium respectively Use the left mouse button and hold it down to manually draw the complete contour or correct an existing contour If the checkbox X Single Frame Mode checkbox is checked then the segmentation is only performed in the current time frame otherwise in all time frames A quick method to toggle between drawing epicardium and endocardium is to use the space button on the keyboard 12 3 7 Translating the segmentation The segmentation can be translated dragged in each slice This is done by using the icon in the toolbar palette Note that the usage of this transla tion is especially useful in conjunction with the import segmentation option in the main menu Then a segmentation from one imaging technology can be overlaid an image of a different image stack if they were acquired using the same coordinate system A practical application is doing the segmenta tion on cine gradient echo or cine SSFP images and overlay that result over late enhancement images Under the segmentation menu it is possible to translate move selected slices towards the base apex 12 3 8 Scale the segmentation In some slices and typically the apical slices scaling the segmentation can be very effective correction Scaling can be done with the
115. n the Shift key while clicking to place end points Finish by clicking with Shift released You are then asked to annotate and give the measurement a label It is possible to refine the position of the measurement by click one of its end points and drag that to the desired position The measurement with its annotation is shown in Figure Under the Annota tions menu it is possible to clear or export all measurements to the clipboard Measurements of ventricular wall thickness is best performed by using the tools for region wall motion analysis described in Chapter Another method to get distances or timing intervals by adding annotation points at different points in space and time Annotation points are added with the icon and export the coordinates and time points of the annotation points to Excel or another spread sheet program and there calculate the distance Annotation points is also useful for marking anatomical landmarks etc For further details see Section 19 2 Timing By using the M mode viewing mode it is possible to make measurements of both timing and distances This is illustrated in Figure on page 89 CHAPTER 19 MEASUREMENTS AND ANNOTATIONS Figure 29 Example of a measurement of the left ventricle diameter 19 3 Volumes Volume of the left ventricle is displayed and updated as soon as you have delineated some slices If the volume was calculated from segmentation in longaxis images this is indicated in a li
116. nce is the generic reference for the Segment project 185 CHAPTER 40 HOW TO REFERENCE THE SOFTWARE e Automated and manual delineation of the left ventricle on MRI images to get LV volume ejection fraction etc should be referenced as 20 or 27 or preferable 19 e Automated quantification of infarct size and transmurality should be referenced as 5 or 4 depending on what mode have been used If weighted mode have been used to quantify infarct transmurality then paper should be used e Flow quantification should be referred to as 19 e Strain analysis should be referred to as 16 e Segmentation of the left ventricle in non gated SPECT images should be referenced to as 23 e Segmentation of defect size of myocardial at risk from SPECT images should be referenced to as 24 e Segmentation of myocardium at risk from T2 STIR imaging should be referred to as 9 e Segmentation of myocardium at risk from cine delayed enhancement should be referenced to as 25 e Measurement of endocardial extent should be referenced to as 26 e Creating polar plots should be referred to as 27 e Fusion data sets should be referred to as 13 40 1 Examples of possible formulations e left ventricular mass and ejection fraction was measured using Seg ment v2 0 R4790 http segment heiberg se 21 e Infarct size were determined using Segment v2 0 R4790 http segment heiberg se 5 e Image analysis w
117. nce of how to handle and develop a large scientific software package As the software grew in capabilities there also started to be a commercial interest in the software However Segment will always be tightly coupled to cardiovascular research and continue to be freely available for research purposes We hope that you will find the software useful in your research and please do not hesitate to tell us what you think about it and come with suggestions for improvements The software has been developed at Home during late evenings and weekends Linki 5ping University Sweden Centre of Medical Image Science and Visualization amp Department of Medicine and Care Clinical Physiology 2002 2004 CHAPTER 4 RATIONALE FOR THE SOFTWARE e Cardiac MR Group Lund University Department of Clinical Physiol ogy 2005 present e The company Medviso AB 2007 present 5 How to Read This Manual Technical documentation always face a certain dilemma whether write for top down or bottom up learners A top down learner prefers to read or skim documentation getting a large overview of how the system works only then does she actually start using the software A bottom learner is a learn by doing person someone who just wants to dive into the software and figure it out as she goes referring to book sections when necessary This documentation is biased towards top down learners And if you re ac tually reading this section
118. nclusion and or exclusion point and only one inclusion and or exclusion object can be segmented at a time 15 4 2 Start the segmentation tool The segmentation is started by placing an inclusion and or exclusion point in the image This is done with the tools and or The inclusion point should be used when a new segmentation or addition to an exisitng segmen tation is the desired result The exclusion point should be used when a part of an object shall be removed from an already exisiting segmentation It is also advantageous to place both an inclusion and exclusion point in the im age when a new segmentation is the desired result since it can give a better estimation of what intensities to include in and exclude from the segmen tation When the inclusion and or exclusion point is placed in the image press the button Grow To set a new inclusion and or exclusion point use the tool once more and the old point will be removed It is also possible to remove the inclusion and or exclusion point with the function and or Y If more iterations is desired use the iterations slider or push the grow button once more If more intensity expansion is desired use the expansion slider to increase or decrease it The expansion speed can be seen in the speed image view after pressing grow 15 5 Object manipulation When you are pleased with an object or part of an object you can store that to a quick pick list by the pushbutton Store Wit
119. ne of text above Volumes of ROIs can be derived by using the numeric multiple threshold analysis described in Section On possible mistake when doing manual delineation of the left ventricle in only diastole and systole is the failure to indicate what time frames that are end diastole and systole respectively This will cause Segment not to show any volumes Selecting diastole and systole can be done by interactively dragging ED and ES in the volume graph or using the Autodetect End systole and End diastole under the Edit menu 19 4 Area Area of ROI s can be derived by using the region of interest analysis tool in Chapter In certain cases area can also be derived by dividing volumes by the slice thickness The area of the ROI s is shown for each ROI in the one slice view In the near future a general area tool will also be added to Segment 90 19 5 FLOW AND VOLUMES 19 5 Flow and volumes Measurements of flows and volumes are covered in Chapter 19 6 Signal intensity Signal intensity can be measured by using the region of interest analysis tools described in Chapter 19 7 Annotation and anatomical landmarks Annotations are added with the icon or under the Annotation menu The points can either be stationary or time resolved i e have different positions in different time frames The stationary points are marked with a bold font To make a pointtimeresolved right click on it and select Make point timere solved from the pop
120. nes 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 Rationale for the Software Developing this software have required a lot of work So what has the ratio nale been for producing new software where there are commercially available software packages that at least partially could do the same thing At the time of writing the core of the program other existing software were simply not good enough Existing software packages did not allow to store the segmentation and regions of interest in a flexible way Existing software packages had no flexible exporting capabilities to al low full usage of automated delineation algorithms A freely available software greatly facilitates and improves possibilities to do multi center studies There will be no company secrets we will always know and be open and tell you exactly how things are implemented This is crucial for doing good research It can serve as a platform for experimenting and testing of various image processing ideas It has been given very valuable experie
121. ng the corners of the square one can select the region One is also presented with a input box where it s possible to enter the area of this region When 191 CHAPTER 43 PLUGINS pressing the ok button the plugin calculate the correct resolution and updates the image stack accordingly Note that this plugin assumes isotrope images 192 44 Implementation Details In this chapter a few implementation details are given There are much more details that are interesting but this is as far as we have got with the docu mentation If you have specific questions please do not hesitate to ask us 44 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 44 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 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
122. ng in the preferences The line between en docardium and epicardium is resampled in 50 steps and the percentage of infarcted pixels are counted 197 CHAPTER 44 IMPLEMENTATION DETAILS Infarct extent is defined as the projected infarcted area on the endocardial surface 26 Lom Y a 7 i where Tert is the infarct extent T is the transmurality of sector i and R is the mean endocardial radius of sector i 44 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 SDremote SD fromRemote 8 The 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 miss
123. ns The functions described in this chapter is in US only for off label use and for investigational use In Segment it is possible to create own plugins and extensions This is further described in 19 and the Technical Manual Currently there are two plugins that are shipped with the stand alone version of Segment 43 1 Image Loader Plugin The image loader plugin is used to load diffrent kinds of images into segment The plugin currently supports the following image formats e JPEG jpg e PNG png e TIFF tif There are two diffrent ways of loading images in the image loader plugin The first way called Load single file load a single image file in a new image stack The second way called Load files from directory loads all files in a directory and places them in a single image stack The images are ordered according to filename and placed in z depth Some information such as resolution that exist in dicom files are not present in these general image formats The image loader plugin will simply guess on default values for these values Sometimes one can use the calibrate plugin to set the resolution to a correct value 43 2 Image Calibration Plugin Sometimes the correct resolution for an image stack isn t known However if one knows the area of some region of the image beforehand one can calculate the correct resolution This plugin helps one do that When loading the plugin one is presented with a red square By movi
124. ntation in all time frames since this leads to better conditions for the segmentation algo rithm However you can select to only perform the LV segmentation in the selected time frame In order to start the segmentation process click on in the LV mode A new interface is open according to Figure where you select the most basal slice and the most epicardial apical slice of the LV The basal limit should be the most basal slice that have left ventricular myocardium at least in some part of the heart cycle If long axis image stacks are available the slice selection can be reviewed in the long axis views In order for Segment to find the long axis image stacks the Image View Plane have to be defined as 2CH 3CH or 4CH The Image View Plane is defined by right click in the thumbnail preview and select Set Image Description The next step is to ensure that the LV center cross is correctly defined in the middle of the LV lumen This is done by review and if needed adjust the orange cross in the short axis view The center cross should be in the middle of the LV lumen for the midventricular slice and the placement in the basal and apical slices is irrelevant After the selection of LV slices and definition of LV center the automatic LV segmentation is started by click on Start LV segmentation The final result from the automatic LV segmentation algorithm is then displayed in the main interface for Segment If needed manually adjustment of the L
125. o pan the image use the tool and move the mouse There are some general tools that are present in all tool modes and these are 41 CHAPTER 10 PROGRAM OVERVIEW x Select slices or image stacks This is the de fault tool Translate ROIs and contours or the whole image if no ROI or contour was clicked Change the size of ROI s and contours Undo last contour edit command Adjust brightness and contrast Hold down the mouse button and move left right to ad just contrast and up down to adjust bright ness of the current image stack By hold ing down the Shift key while pressing the mouse button the adjustments also affect ev ery other image stacks in the current view and sets the absolute values of their contrast and brightness to be equal to those of the ac tive image stack Contrast and brightness of the current image stack can also be adjusted without first clicking the icon by instead us ing the middle mouse button 10 10 1 Left ventricle tools The left ventricle tools are shown in Figure Colors are used to indicate endocardium red or epicardium green On the first row from left to right 7 is used for an interpolated contour mode to click out points to control the endocardial contour To close the contour and interpolate a line between the points shift click in the image The points can interactively be dragged The second tool is used to man ually draw the endocardium The third tool is to
126. of the GUI you can select which parameter to plot The volumes presented in Volume panel of the GUI represents flow inte grated between the two vertical red bars These bar can interactively be moved with the mouse to control the range of the integration Forward vol ume is the volume of the flow integrated only over the time frames where the 108 23 2 PLOTTING THE RESULT OF THE FLOW ANALYSIS Figure 33 Example of flow plotting GUI Plotting parameter can be selected in the upper right corner of the GUI The flow integration is performed between the two red bars net flow is positive forward Backward volume is the volume of the flow integrated only over the time frames where the net flow is negative back ward This should be contrasted to the flow parameter Forward Backward that plots simultaneously the flow that goes forward and backward of the region of interest Note that there can be significant backward flow in one time frame even though the net flow is forward in that very time frame An example on the latter is shown in Figure The sum of the two curves is the same as the net flow that is shown in Figure It is also possible to plot the Velocity over time and this is shown in Fig ure The error bars denote the standard deviation of all pixels in the ROI of that particular time frame Another possibility is to plot the max or min velocity in the ROI over time It is also possible
127. often required to synchronize image stacks in time and slice This can be done by using the Shift key Shift left right key shows previous next frame and synchronizes all visible image stacks in time For image stacks that have different number of time steps the nearest time frame is shown Shift S and Shift D toggles between systole and diastole in all visible image stacks 10 9 Loading and storing images The top left section of icons contains functionality to load and save image data The first icon amp opens a file loader GUI described in Chapter 9 The second icon opens the patient database described Segment Database User Manual The third icon saves all the loaded image stacks to one file The fourth icon 2 opens a connection to a PACS server see Segment Database User Manual 10 10 Tool palette The tool palette is located at the lower right corner of Segment main graph ical user interface The tool palette have several modes in which different tools become available The current mode is indicated as black text on blue background The current active tool is indicated by displaying the tool in a darker gray color Generally with few exceptions all functions in the program only applies to selected slices Selected slices are indicated with a yellow box in the montage view The functionality of selecting slices can only be used in the montage view An alternative to select slices is to use the short key Ctrl A that selects all slices T
128. omography Steady State Free Precision Stroke volume Time of Flight Velocity Encoding limit 13 7 System Requirements In this chapter the hardware requirements for the software are outlined Pos sible bottlenecks are in order of likelihood lack of RAM memory CPU speed and I O network or disk transfer rates 7 1 Operating system Segment is available both as a precompiled application and also a source code version Precompiled versions are available for the following platforms e Microsoft Windows It will run on any of the following Windows 2000 Windows XP 32 bit Windows XP 64 bit Windows Vista 32 bit Windows 7 32 bit Windows 7 64 bit Windows 8 e The Segment have been reported to run well on Mac using Parallels The source code version is available for the following platforms e Windows 32 e Windows 64 e Linux 64 To run the source code format you need Matlab R2011a or later 7 2 Hardware requirements The list below are the recommended hardware requirements To run a clinical versin of Segment you need at least the specifications indicated below e A fairly recent computer with 4 GB of memory or more e Harddisk with at least 500 MB of available space The program Mat lab Compiler Runtime takes about 450 MB another 20MB is taken by the program e Graphics card supporting both DirectX and OpenGL hardware accel erated is recommended Systems with two screens is recommended for clinical usage of S
129. on again by select Analyse 9 Manually change the short axis slices for the bullseye division by select Set short axis slices 10 Click on export buttons to export result to spreadsheet 160 35 Image Fusion Module The functions described in this chapter is in US only for off label use and for investigational use Details of this Fusion Module is given in Ugander et al 18 The image fusion tool is used to compare and fuse one anatomical and one functional image stack Currently the tool is restricted to rigid body trans lation and rotation An example of the fusion GUI is shown Figure The leftmost panel is the anatomical image stack the middle the functional image stack and the rightmost the fusion image stack lol Anatomical Functional Fusion A Manual co registration ofthe functional image set Translation in transversal image pixels Reset contrast Reset All Figure 61 Example of the image fusion GUI To start the fusion tool select Fusion of Two Image Stacks under the Fusion menu You will then be prompted for which anatomical and functional im age stacks to fuse You select by entering a number that are the same as the 161 CHAPTER 35 IMAGE FUSION MODULE thumbnail order from left in the main Segment GUI If the anatomical im age stack contains a segmentation this will be shown both in the anatomical and the functional image stack
130. ons one slice EH montage or all slices HH mon tage view in rows and 44 m mode view Each of the different viewing modes will be described in details below It is possible to view the same im age stacks in different viewing modes simultaneously The number of image panels can be selected by the icons O 04848 lH H Bor under the View menu The icon da views information about the patient It also also possible to enter adjust the patient information Commonly this is used to add patient height to be able to calculate BSA The icon brings up an interface for saving and loading user specified views This allows users to save their favourite combination of stacks to view for use with any image set It is also possible to associate each saved view with a specified hotkey When loading a saved view for a new image set Segment automatically looks for the best matches among the current image stacks taking into account such properties as image type view plane time resolution etc This interface also enables the user to save and load specific contrast brightness settings in absolute values which can also be assigned a hotkey The section E 0 K ie EE X ZG 3 controls the visibility of pins con tours from other image stacks endo epicardium contours region of inter ests delineated infarct regions measures and annotations center point and 35 CHAPTER 10 PROGRAM OVERVIEW image plane intersections respectively
131. or investigational use There are numerous possibilities to manipulate image stacks This chapter describes the tools found under the Image tools menu in the main menu Many of these operations are not undoable One workaround is to before applying the intended tool right click on the image stack thumbnail and se lect duplicate image stack By doing so you do not need to reload the image stack at least 17 1 Crop image stack This functionality is useful to crop the images to reduce memory requirement This functionality is not available under the image tools menu but as a tool in the tool palette Y Note that this function is not undoable 17 1 1 Autocrop all image stacks There is also a functionality to automatically crop all image stacks The icon for this NS is found next to the crop icon 17 2 Remove time frames There are several suboptions to select exactly which time frames you wish to delete Note that when you have removed time frames you should also save the image volume since it is not possible to directly load the segmentation if it is stored as a separate seg file Note that this function is not undoable 17 3 Remove slices It is possible to remove all selected slices or all slices except the selected slices When removing slices note that you may not be able to import a segmentation to the current image stack since the number of slices will not 75 CHAPTER 17 IMAGE TOOLS match When removing slices and yo
132. oral distance from the moment when the tan gent of the Aortic ascending flow curve is equal to zero to the moment when the tangent of the Abdominal Aorta curve is equal to zero This distance is displayed as a dotted portion of the black line along y 0 in the plot The values for aortic length time between upslopes and calculated velocity are displayed in the GUI and can be exported to a spreadsheet by clicking the Export button 117 CHAPTER 24 PULSE WAVE VELOCITY ANALYSIS ee am 7 7 400 j 300 T 200 ma E 100 jaz E f Sigma oo fs 0 100 200 300 400 500 600 700 800 T ms Aortic Length 232 0 mm Delta T 54 4 ms Pulse Wave Velocity 4 27 ms export Figure 39 GUI for Pulse Wave Velocity Analysis On the left is the image containing the measurement of Aortic Length On the right is a plot of flow curves along with their respective tangents 118 25 Stress Analysis In earlier versions of Segment there were a special stress viewer available This have been removed since it s functionality is now directly available in the normal viewing capabilities of Segment synchronized viewing of several image stacks It is possible to place four or more image stacks on the screen simultaneously and play them synchronized in the same speed by the icon E Other functionality in Segment that could be used to analyse stress images is the report per slice functionality described in
133. ormed once and should generally not be necessary when upgrading to a later version of the software Note For some operating systems it is required to reboot the computer after installing the MCRInstaller We therefore strongly advise all users to reboot the computer after installing the MCRInstaller 8 1 2 Installing Segment Download the file called something like install Segment 2px Ryyyy exe where 2px is the version number and Ryyyy is the revision number Place 17 CHAPTER 8 INSTALLING AND UNINSTALLING Utgivare The MathWorks Inc Typ Program Fr n C Users Einar Desktop MCRinstaller_7p15_win64 exe Lose en Y Yarna alltd innan den har filen ppnas Filer du hamtar fran Internet kan vara anv ndbara men den har sortens e fil kan eventuellt skada datorn Kor bara programvara fran utgivare du itar pa Vilka risker inneb r deta Figure 1 Click on Run or K r MATLAB R Compiler Runtime 7 15 reqares that the following requirements be installed on your computer prior to stalin this application Click OK to begin installing these requrements Pending VOREDIST v40 64 Pending VOREDIST 54 Figure 3 Click on Install 18 8 1 INSTALLATION OF STANDALONE VERSION FOR WINDOWS JG MATLABIR Compiler Runtime 7 15 InstallShield Wizard MATLAB Compiler Runtime The Instalishield R wizard will install MATLAB R Compier Runt me 7 15 on your computer To continue click Next WARNING This program is
134. ort DICOM CD ROM s see Section 20 5 25 CHAPTER 9 LOADING IMAGE STACKS iol xi aog Secrinique Path C Medviso IV Store directory cache information Patient and image series details Type ORIGINALYPRIMARY M_FFEIM FFE IV Use cached directory information Seq I Fiter files F mat dem Ser sbFE BH4ch Ser 601 SliceLocation 0 AcquisitionDate 20061204 AcquisitionTime 162252 89 Name Hidden ID BirthDate Sex M S i SE0501 30 files Age HeartRate 53 SE0701 630 files SE1401 80 files Preview Position DICOM I Stable but slow DICOM H DICOM info 7 win roe mas coca ss AREA ce Figure 5 File loader GUI 26 9 1 LOADING DICOM FILES 9 1 Loading DICOM files 9 1 1 Loading DICOM files When loading MR DICOM files Segment assumes that the files are sorted so that each image series is stored into one folder Each folder may then contain one or many DICOM files This is illustrated in Figure 6 Patient Series001 DICOM files Series001 DICOM files Series001 DICOM files Serieso01 DICOM files Figure 6 Files needs to be sorted so that each image series are stored into a separate folder If the files are not stored in this fashion then there is a sorting utility available described in Chapter DICOM is an loosely structured file format and direct reading from DICOM files is slow C
135. oso ers rr E 21 8 5 2 Setting window positions 22 8 5 3 Patient database 64 5 acacia ss 22 8 5 4 PACS connection 0 000 eee 22 8 6 Uningtallation 2 da ie woe u AAA 23 8 6 1 Uninstalling for Windows 23 8 6 2 Uninstallation for source code 23 8 7 Trouble shootingl zu 2 2 0 a ee 20 ss 23 25 Cod ee e ee ee 27 9 1 1 Loading DICOM files 27 9 1 2 Loading SPECT DICOM files 27 nn 27 9 1 4 Tips and trieks a cese e ee ee ee eee 29 9 1 5 Loading images from CD 29 9 1 6 Graphical image series selection 29 917 DICOM details 2 0004 30 9 18 Unstructured filesl soo rr rr rr rr rr se es 31 9 2 Matlab format details lt lt ss 8 au ae re 31 33 Su a a a 35 A ee TR ee 36 dar a A A ad Hw Sh 36 Re Ge lee Sed po e ee ee 36 eee AR eee ew ee Ae ee Sod BM BE SS 38 nennen 40 10 7 Playing images as accine loop 0 40 Sim uh BOE ee Bas 41 ii CONTENTS 10 9 Loading and storing images 41 10 10 Tool palettel ooo 2 2 24 rr rr en en E ss es 41 1 10 1 Lett ventricle tools 2 0244 Se ye sea an sees 42 10 10 2 Right ventricle tools 43 10 10 3 Viability Scar toolsl zu EA a 44 10 10 4 Miscellaneous tool model 45 EEE EEE 45 10 11 View Tool model soda 2 0 1 00 0a Bewer 46 10 12 General view and report
136. oup image series to one image stack Image series that are to be grouped are selected by holding down the Shift key while mouse clicking or by using the middle mouse button Thereafter press the push button Group Selected Grouped image series are shown with a green outline Multiple image stacks can be selected for loading or grouping by clicking and dragging over the selection When finished selecting image series press Load To speed up the process this operation the generation of the thumbnails is cached Note that when using this tool to load the image then there is no cropping of the images done and that is highly recommended to crop the images during 29 CHAPTER 9 LOADING IMAGE STACKS the image analysis process Also note that if multiple directions is detected in the dicom folder all the different directions are loaded as separate image stacks lolx Patient into Series info Name KJ43 Pathname Serie0026 ID Images 15 Select all Age Seriesdesc ViebilitetM3D_MCSsa Bee SEE Sex M Venc Acquisition date Unselect all Acquisition time 000000 r Image series Figure 7 Graphical image series selector 9 1 7 DICOM details First of all remember that DICOM is not a well defined standard I have tried hard to make Segment to work with DICOM files from different imaging device manufacturers It is currently tried on General Electric MR scanners Siemen
137. r This is very important since it is necessary that we can prove to granting organisations that this project returns scientific output and has a significant impact to the scientific community A reference should encompass both the name and version of the software and a reference to a suitable scientific publication about that function in Segment It should also be indicated that the software is free for research purposes and the address homepage of the software http segment heiberg se You should reference the software differently depending on what part of the software that have been used This list is subject to change after submitted papers are accepted Always check the homepage for the latest information regarding this issue In doubt please do not hesitate to contact the author or place the generic Segment reference 19 Note that referencing the software is mandatory also for abstracts to scien tific conferences It shortage of space reference the software as something like Images was analyzed using the freely available software Segment http segment heiberg se In extreme shortage of space such as conferences where the word limit is lt 350 words then reference may be omitted in the abstract text but should be included in the oral presentation and or poster The following list describes various usage of Segment and how it should be referenced e General usage of Segment should be reference 19 This refere
138. ract contour Rotate Inner Outer F crop N N 10 20 320 40 10 20 30 40 50 0 10 20 30 40 50 60 o 100 contour a gt a gt ac a gt Figure 64 GUI for perfusion analysis after motion correction The two plots on the right side of the GUI show the upslope curves of the current sector selected from the pop up menu which are calculated using a Gaussian filter on the measured values The width of this filter can be adjusted using the slider labelled Smoothen curve making the curve sharper or smoother By checking the box X Show bloodpool a curve of the blood 167 CHAPTER 36 PERFUSION ANALYSIS pool is shown in red in the same plot The bullseye plot below the curve plots displays the sectorwise quote between the maximum stress and rest up slopes normalized with respect to the respective maximum upslopes of the bloodpool curves The quote values are also shown in text next to the bulls eye plot and can be exported to a spreadsheet by clicking the Export button 168 37 Native Bruker Reader Module The functions described in this chapter is in US only for off label use and for investigational use This module to load native Bruker files is a commercially available module to Segment The structure files and directory of the Bruker Paravision file format is given in the Imaging Wiki http imaging mrc cbu cam ac uk imaging FormatBruker Some further detai
139. rame of the image sequence is displayed The icon kl Shift left shows previous frame but applies to all visible image stacks It displays the previous frame for the current image stack and tries to find the corresponding time frame for all image stacks The icon AN left displays the previous time frame for the active image stack You can also use left arrow button The icon bk plays the active image stack sequence as a cine loop The icon I right shows the next frame for the active image stack You can also use right arrow button to show the next frame The icon Ib Shift right performs the same operation as YI but forward in time instead Control and arrow keys show previous next frame for all image stacks The icon increases the playback speed and decreases the speed Another convenient method to quickly move between time frames is by clicking in the volume graph Here you can also interactively drag which time frame is used as end diastole ED or end systole ES You can also switch between systole and diastole by using the hot keys d and s respectively Yet another way to scroll between time frames is to use the mouse wheel and at the same to press Shift The icon O gt allows the user to perform manual delineations while the current slice is played This is very useful for a better understanding about for instance the papillary muscles 40 10 8 SYNCHRONIZING IMAGE STACKS 10 8 Synchronizing image stacks It is
140. re mul tiple image stacks can be visualized side by side The current active image stack is outlined with an orange thick line To make another image stack active simply click on the image stack with the mouse pointer A thumbnail image is shown for each loaded image stack To view an image stack drag the thumbnail down to the main viewing area To scroll through the thumbnails either use the slider or press Ctrl while scrolling with the mouse wheel The upper right corner is occupied with a reporting panel where quantita tive details about the current image stacks are shown There are two rows of icons The top row contains icons that applies to all loaded image stacks whereas the bottom row contains icons to applies to the current active image stack only Middle right part of the user interface is occupied by a volume curve and a time indicator This graph area shows left ventricle volume versus time red left ventricle muscle volume green papillary muscle volume blue One easy method to adjust the displayed time frame is by clicking in this graph You can also interactively drag which time frame that is taken as end diastole ED or end systole ES Just above the volume graph a list box with assumed long axis motion is located In this example the long axis motion is automatically calculated under the assumption that the left ventricular mass is constant over time The program selects the long axis motion amplitude that best fits this
141. re reduction 4 apparent absence Gated Next Prev lay top Frame rate a slower faster each time frame over cardiac cycle Normalize counts Save and Exit Correct LV segmentation More basal GJ More apical r Correct LV segmentation More basal El More apical Figure 56 The perfusion scoring interface The LV is divided into 17 seg ments accoring to AHA model 151 33 Cardiac CT Module The functions described in this chapter is in US only for off label use and for investigational use Currently we are working on a Cardiac CT Module that will be useful for automated segmentation and image analysis of CT images Currently this functionality is only available upon request In the module functionality for automatic segmentation of pericardial sac whole heart CT automatic identification of the coronary ostia and auto mated bone segmentation The automated segmentation of the pericardial sac will be highly useful for visualization of the coronary arteries in conjunc tion with the volume rendering module that is work in progress Please contact Medviso AB to get a demo of these features 153 34 Strain Analysis Module The functions described in this chapter is in US only for off label use and for investigational use 34 1 Velocity Encoded Imaging The strain analysis module uses velocity encoded MR images to calculate myocardial strain The module have be
142. removes the manual corrections made with the Zor By default manually added mar regions shows up in green and manually deleted areas in blue 105 23 Flow Analysis This functionality may depend on your MRI scanner Currently it has been tested using Siemens Philips and GE scanners When flow image stacks are displayed the screen should now similar to what is shown in Figure 32 On the left image panel the magnitude image is shown and on the right image panel the phase image is shown When a flow image stack is selected a white frame around both the magnitude image and phase image is drawn in the thumbnail preview area This helps to keep track of which phase images belongs to which magnitude images ly Aortic ase flow 6 8 cm Slice 01 Time 157 mm Flow through plane Figure 32 Example of main GUI in flow mode 23 1 Automatic segmentation of flow ROT s The suggested method is to select the ROI tool Then draw a ruff outline of the vessel contour Thereafter start the automated vessel tracking and refine This is done by pressing Ctr1 T Another method to automatically segment a vessel is to drag the center cursor white to the approximate center of the desired vessel and press Ctr1 G 107 CHAPTER 23 FLOW ANALYSIS or Auto delineate a vessel under the Segmentation ROl and Flow Tools menu The vessel is automatically delineated and you are asked for an appropriate label Deleting renaming recolorin
143. res e Support Details about the support is given in Chapter 41 e Report sheet generator In this module it is possible to print a report sheet with a results and free text annotations as a patient report This is described in Chapter CHAPTER 2 LICENSE TERMS 2 3 Native Bruker file format reader The Native Bruker file format support module allows you to directly load Bruker files into Segment This is described in Chapter 37 Segment patient database This allow you to easily find and load your patient images This module is further described in Segment Database User Manual Segment DICOM server module This module allows Segment to work as a standalone workstation and receive images directly from the scan ner a hospital PACS or another DICOM workstation This module is further described in Segment Database User Manual Segment PACS connection module This module allows you to down load and export images directly to a PACS system This module is further described in Segment Database User Manual Sectra Plug in Module This will allow you to run Segment as a plug in to Sectra PACS Commercial research non human images There is also a non FDA approved version for commercial purposes of Seg ment available This license type is intended for commercial R amp D compa nies or industry sponsored trials where the majority more than 50 of the funding comes from a commercial sponsor 2 4 Future modules Then there
144. rmed for the rotated image stacks V 44 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 195 CHAPTER 44 IMPLEMENTATION DETAILS more note that these numbers are valid for healthy myocardium ex vivo what happens in for instance infarcted regions is not shown in the literature Therefore usually it is better to report volume instead of mass 44 6 Calculation of BSA The formula used is based on Mosteller wxh BSA y 2 E 3600 2 where w is the body weight in kg and h is height in cm 44 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 44 8 Wall thickness Currently wall thickness is defined as the thickness along a radial spike from the endocardial or the epicardial center depending on setting 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
145. rther details see Section 12 3 17 14 View Image details This function copies the most important image details to the clipboard It is the same as the icon 79 CHAPTER 17 IMAGE TOOLS 17 15 View and adjust image details By using this menu option it is possible to adjust image details Parameters that can be adjusted are Slice thickness Slice gap Resolution in x direction Resolution in y direction and time increment 17 16 View and adjust patient details This menu option starts a graphical user interface where it is possibly to view adjust Patient Name ID birth date acquisition date age height weight sex The pushputton Apply to all applies the changes to all image stacks that are loaded to memory By entering height and weight BSA is automatically calculated 17 17 Remove subject identity By using this menu option all patient data are removed from all image stacks This is useful when sending data to a different center or for bug report purposes This function is not undoable Removed items are patient name id birth date acquisition date filename and original filename 17 18 Calculating image histogram Image histogram can be calculated by using tools found under the ROI menu For further details see Section 18 6 80 18 Region of Interest Analysis The region of interest ROI functionality can be used for a wide range of possibilities To select the ROI mode you can use the hot key S
146. s CT MR PET and Philips MR scanners Bruker MR Suinsa PET Furthermore various PACS manufacturer might corrupt the files in different ways 30 9 2 MATLAB FORMAT DETAILS The DICOM reader does not support JPEG encoded images or big en dian DICOM files However when images are imported into the patient database or sorted by the DICOM sorter they are converted on the fly and can be read by Segment DICOM reader There are some short cuts taken in the fast loader e The spacing in time is assumed to be equal between all frames when loading time resolved images This may be violated if the scanner rejects some beats in a perfusion image serie for instance e The spacing in slice is assumed to be equal between all slices when loading image stacks with multiple slices e When you have loaded a rotated image stack you need to tell Seg mentabout it It is done under Image Tools and View Adjust and Image Details A rotated image stack is a set of slices that are rotated around a central axis Then subsequent analysis will assume that the data is a rotated image stack When you view the data in single slice view Lla cyan line are drawn with the rotational axis indicated To get correct volume estimates it is crucial that this line co incides with the true axis of rotation To achieve this you may have to flip the image stack see details in Section 17 7 9 1 8 Unstructured files Some systems Siemens depending on platform versio
147. s possible even if they are attached to the wall Details on how to manually include exclude the papillaries are given in Section 12 1 2 Mitral annulus Long axis motion of the left ventricle is a very important component to achieve correct ejection fractions and volumes Long axis motion is ac counted for in the automatic LV segmentation algorithm The long axis motion direction is assumed to be orthogonal to the slice direction The long axis direction is shown in Figure In the most basal LV slices the algorithm defines the LV segmentation with the long axis motion in mind 12 2 Start the segmentation process Before starting the automatic LV segmentation process make sure that the basal apex orientation is correct The most basal slice should be in the upper left corner If not then select Image Tools Flip z and x as described in detail in Chapter Also make sure that correct Image Type is selected when loading the image stack MR SSFP CT This can also be set afterwards by right clicking on the image stack thumbnail image and select Set Image Description If the checkbox X Single Frame Mode checkbox is checked a l CHAPTER 12 SEGMENTATION OF THE LEFT VENTRICLE Longaxis direction Figure 18 Three dimensional view of the left ventricle showing the long axis direction message box questioning if you would like to perform LV segmentation in all time frames is asked It is recommended to do the LV segme
148. 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 44 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 viable 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 7 rosie Pas 1 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 perfo
149. segmentation from multiple mat filesl 20 4 Sort Folder of DICOM files 2 2 2 2 rr nern 20 5 Copy and Sort Images from CD to Data Folder 20 6 Create DICOM cache for folders recursively 20 7 Create thumbnails preview recursivelyl ere ee if bonehead EUER EEE eek 21 Viability Analysis 21 1 Automatic mode weighted SCJ or FWHM 21 2 Manual mode 21 3 SD from remota 21 4 EM algorithm 2 223444 scr rss eh 44404 4 21 5 Technical details ooo 2 oo oo nn 21 6 Grayzone Analysis 2 cs 0 su sen ne a nn 21 6 1 Gray Zone analysis by weighted method 21 6 2 Gray Zone analysis by ROI method 22 Myocardium at Risk Analysis 23 Flow Analysis 23 1 Automatic segmentation of flow RODs 23 1 1 Refine oo 8 5 3 8 2 Me Se a ES YORE ESE REG Sa 23 1 2 Refine and propagate so lt lt vn 23 13 Shrink How RO 2 eo eee Rae we ee 23 2 Plotting the result of the flow analysis 23 3 Compensating for eddy current effects 234 Phase unwrapping 2 44 cee ee ee eRe Soo Be aa 23 4 1 Automated unwrapping 23 4 2 Manual unwrapping cese dans de o 93 93 93 93 93 95 95 95 95 96 96 96 99 101 102 102 103 103 103 103 104 105 CONTENTS 24 Pulse Wave Velocity Analysis 25 Stress Analysis 26 Regional Wall Analysis 26 1 Radial contraction versus timel
150. shown at a time You can then browse between slices by up down arrow keys Right and left keys displays next and previous time frames In this view intersecting image planes that also are shown The intersection are indicated with a white or an orange line Orange line indicate intersection with the current active image panel To hide view the plane intersections use the icon In this view intersec tions with contours drawn in other image stacks are also shown For instance if the short axis stack is segmented the contour will also be visible in the long axis image This is illustrated in Figure This is very useful to delineate 36 10 4 ONE SLICE VIEW Figure 9 Screen shot of the program showing an image stack in montage view 37 CHAPTER 10 PROGRAM OVERVIEW structures that might be difficult to see in only one image plane The contour intersections can be hidden by using the icon The contour intersections are only visible in one slice view mode Note that different breathing position may cause the image stack not to align properly Figure 10 Contours are visible in other image stacks as dots This is very useful to delineate structures that might be difficult to see in only one image plane 10 5 M mode view Another_viewing option is the M mode Example of this view is shown in Figure The viewing option is chosen by the icon ZH In the image panel to the left one slice is displayed To view a different slice
151. st menu option deletes the current last drawn or modified ROI The second menu option deletes ROI s with a name matching a specified template A menu of possible ROP s that can be deleted are shown 18 5 ROI analysis It is possible to plot and export the following parameters over time e Mean signal intensity e Standard deviation of signal intensity e ROI area e ROI area based on pixels e Minimal signal intensity Maximal signal intensity 83 CHAPTER 18 REGION OF INTEREST ANALYSIS Figure 26 Graphical user interface for ROI analysis 84 18 6 ROI HISTOGRAM An example of the user interface is shown in Figure In the ROl selection panel the ROPs to plot can be selected If the checkbox amp Use ROI s only from this slice is selected then only ROI s in the current slice are shown If the checkbox Use normalized values is selected the the values are shown in the Segment s own internal normalized representation Otherwise the values are recalcu lated back to the pixel values in the DICOM files In the View panel it is possible to select to plot min max values min max slopes or Full Width Half Maximum FWHM If the checkbox X Smooth curves is selected then the curves are smoothed before slopes and min max values are calculated The smoothing is applied is a Gaussian smoothing kernel The smoothing parameter o is adjustable with the slider and the edit box By using the Plot fi
152. stole and diastole An example of segmentation of the right ventricle is shown in Figure 97 CHAPTER 13 SEGMENTATION OF THE RIGHT VENTRICLE Figure 20 Top Segmentation of the right ventricle in diastole in a short axis image stack Bottom Segmentation of the right ventricle in systole in the same short axis stack Note the relative large long axis motion 98 14 Segmentation of Long Axis Images Segmentation of the left ventricle as well as any other chamber can be done by manually outlining the object in longaxis images This is a fast alternative to manual drawing on short axis images Contours need to be present in at least two image stacks labeled 2CH 3CH or ACH to enable volume calculations Please note that the image stacks needs to be labeled view the correct view To label the images right click on the thumbnails and select Set Image Description Figure PI illustrates the concept of segmentation in long axis images 14 1 Click an image to show point location in all views To provide a better estimation of the three dimensional volumes when draw ing in longaxis images there is a tool that allows the user to click an image to show the location of the clicked point in every active view This tool XA is found in the Misc toolbox 59 CHAPTER 14 SEGMENTATION OF LONG AXIS IMAGES Figure 21 Illustration of the process of drawing segmentation in long axis images 60 15 Segmentation of General Objects
153. t in red color Finally the checkbox X Outline determines whether the object outline displayed in yellow color is shown or not 61 CHAPTER 15 SEGMENTATION OF GENERAL OBJECTS E General 3D 4D segmentation tool gt File Edit Objects Tools Segmentation View a m 29008 SYET Mor Show Level set segmentation as MIP Outline Adjust speed map Y Interaction Selection Radius 1 5 4 Curvature 0 45 af Gradient o f Penrad 4 4 Smooth 4 4 ji _Defauits Go few Go medium Go many Prototype based a Startinde Aorta prototype Parameters Region growing Expansionfactor 2 4 gt a terstions log 6 4 gt 1 N _ Grow Object manipulation OR Up AND Down NOT Delete eat L Sort Rename Si Smooth Label Store pit Y Plot polygons 7 Reduce patches _ Plot 30 i Volume Undo 2i Trreshold Close Figure 22 Graphical user interface for general object segmentation 62 15 2 LEVEL SET SEGMENTATION 15 2 Level set segmentation 15 2 1 Algorithm The algorithm is based on a very fast level set algorithm 2 From a seed point or set of seed points the object is expanded outwards The expansion is stopped at edges or regions with low signal intensities The expansion is also penalized for large cur
154. 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 function 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 th
155. 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 44 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 193 CHAPTER 44 IMPLEMENTATION DETAILS 194 e Number of slices This is calculated from the presence of different slices based on the DICOM tags ImagePosition and ImageOrientation 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 space 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 bac
156. the program will take all files below the selected input directory including its subdirectories The input output folders should preferably not overlap Each file will be named according to the name template followed with a 5 digit number The function DICOM tags asks for a filename and displays all DICOM tags in that particular file The checkbox X Stable but slow DICOM controls what DICOM interpreter is used in the sorting operation If you select the checkbox X Create DICOM cache then the program will create cache files that are used when loading DICOM data into Segment This will significantly speed up loading and is therefore recommended For more details of caching of DICOM files see Chapter 9 The checkbox amp Ignore empty DICOMs allows the user to leave out files where the AcquisitionDate tag is either empty or broken which is an indication of 94 20 5 COPY AND SORT IMAGES FROM CD TO DATA FOLDER an empty file If a series is broken up into parts with separate series numbers X Sort by series description sorts all files with the same series description into the same directory If this is selected Include acquisition time can be used to include acquisition time in filenames thus making the time order of files in the series directory easy to follow 20 5 Copy and Sort Images from CD to Data Folder This function is ideal to us
157. tient ID Age Length Weight Sex BSA Heart rate R R interval LVM in ml LVM in g EDV ESV EF LVM from viability images Scar percentage Scar in ml measured on viability images Furthermore for each ROI in the image stack the name of the ROI and the total volume is reported When EDV and ES is not exported see Section 19 3 for hints 20 11 Export Information from multiple mat files This function exports imaging information from multiple mat files Example on exported information is e ImageType 96 20 11 EXPORT INFORMATION FROM MULTIPLE MAT FILES Image size Resolution Slice thickness and slice gap Time increment between Information whether the file contains infarct sizing flow information segmentation 97 21 Viability Analysis The functions described in this chapter is in US only for off label use and for investigational use The viability tools can be found under the MR menu in Segment The method used for automated delineation of infarct is described in 4 It uses a new paradigm in analyzing delayed contrast enhancement MRI Instead of treat ing each pixel as dichotomously infarcted or not infarcted pixels are weighted with their signal intensity The new method delineates a larger area than the previous method 5 It should be noted that even though it delineates a larger area this should not be compared to manual delineation since the darker pixels are given a lower weight As a graphical ill
158. tion slider or take the start ing sector as the sector that is closes to the annotation point Start Sector How to place annotations see Section 19 7 121 CHAPTER 26 REGIONAL WALL ANALYSIS Sector 1 Sector 2 Sector 3 Basal Apical 0 0 5 1 0 5 1 Time Time Time Contraction emis 6 4 2 0 2 4 Expansion j cm s 6 Sector 6 Sector5 Sector 4 Basal Apical 0 0 5 1 Time Time Time Figure 40 Radial velocity versus time in six sectors Note the apical to basal gradient in the onset of the radial contraction Report per slice allthickness mm T T Sector 1 Sector 2 Sector 3 Sector 4 Sector 5 Sector 6 Radial velocity Radius Export Play Next Prev Figure 41 Wall thickness over time in a healthy subject 122 27 LV Sphericity Analysis LV sphericity can be calculated from the Report menu The sphericity of the left ventricle is defined as the maximum short axis di ameter divided by the length of the ventricle This calculation is performed separately for ED and ES and for each of these timeframes it is required that there exists LV endocardium segmentation in an open short axis image stack as well as an image stack containing a measurement labelled End Diastolic Length and End Systolic Length respectively The values of diameter and length of the ventricle and the calculated spheric ity are displayed
159. tion with the pen for endo cardium segmentation amp and epicardium segmentation 143 CHAPTER 32 SPECT ANALYSIS MODULE 32 3 Automatic quantification of myocardium at risk To perform automatic segmentation of the myocardium at risk MaR in the segmented left ventricle use the function Auto Detect MaR under the Myocardium at Risk and SPECT menu The MaR in the SPECT image are defined as a region with low intensity The intensity limit that define the perfusion defect are set by the MaR preferences as described in the next section An example of outlined MaR are shown in Figure From the segmentation the MaR is quantified by percentage extent absolute volume in ml severity of the defect and total perfusion deficit TPD The TPD value includes both extent and severity of the MaR and ranges between 0 no perfusion defect to 100 severe perfusion defect in the whole LV Figure 51 An example of a segmented left ventricle with myocardium at risk outlined The red line is the endocardium the green line the epicardium and the yellow line the perfusion defect 32 3 1 Define RV center In order to calculate the TPD value for each of the sections of the LV supplied by the three main coronary arteries LAD RCA and LCx the placement of 144 32 3 AUTOMATIC QUANTIFICATION OF MYOCARDIUM AT RISK the right ventricle in relation to the left ventricle need to be defined This is done by estimating th
160. trademark of the Mathworks Inc http www mathworks com 6 3 Abbreviations 2CH Two chamber view 3CH Three chamber view 4CH Four chamber view 3D Three Dimensional 11 CHAPTER 6 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 12 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 6 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 T
161. train From Velocity Encoded Imaging under the Strain menu Before calculating strain the image type have to be set to either Strain 2CH TFE or Strain 2CH FFE and similar for 3CH and 4CH This is done either upon loading or by right clicking on the corresponding thumbnail images and select Set Image Type 34 1 1 Strain calculation The strain in a long axis velocity encoded image stack is calculated by using the function Strain Tool under the Strain From Velocity Encoded Imaging un der Strain menu Note that you need to manually outline the myocardium in end diastole first The function calculates segmentation and strain in all time frames It also opens a new graphical user interface that make it possible to analyse visualize strain in the image An example of such a GUI can be seen in Figure To select which strain or displacement parameter to analyse mark one of the parameters in the listbox in the figure The 4 alternatives are e Total Strain e Radial Strain Longitudinal Strain e Shear Strain To see how strain changes over time there are three buttons in the figure to use Prev that step one time frame backward in the heart cycle Next that step one time frame forward in the heart cycle and Play plays a movie of strain over the whole heart cycle The buttons Min and Max produce a figure of minimal respectively maximal strain in each pixel over time T
162. u want to use the data set later be sure to save the image stack Note that this function is not undoable 17 4 Fake in extra apical or basal slice In some instances the most basal or the apical slice may be missing due to improper scan planning This should be avoided and be reported back to the scanning operator However if it still occurs the image set might be possible to rescue the image stack with this operation It inserts a copy of the basal or apical slice and the segmentation The reason that this might work is that it might be possible to copy the delineation of the basal slice in end diastole to the second most basal slice in end systole 17 5 Manipulate light contrast Once loading image data from DICOM files Segment internally converts the image data to the range 0 1 The conversion factors are stored and the original pixel intensities can thus always be recovered 17 5 1 Permanently apply light setting When adjusting contrast and brightness the changes only affect the on screen appearance With this option the current light setting is permanently ap plied to the image stack This will then have impact on subsequent image quantification Note that this functionality is not undoable 17 5 2 Normalize image data When loading image stacks from mat files this check is not performed Nor malize image data will do this process This process is currently not undoable even though all the required data is stored 17 5 3 Inv
163. ugh the slices from the top to the bottom If this requirement is not fulfilled use the function Flip z also Flip in x under Flip amp Rotate Image tools e The septal part of the heart have to be in the left side of the image A segmented left ventricle is shown in Figure The endocardial segmen tation is illustrated as red lines and the epicardial segmentation as green lines 32 2 1 Manual corrections If the results from the automatic left ventricular segmentation algorithm is not satisfying the user can do manual corrections This can be done in four ways e Crop the image stack using the icon je find in the lower right panel in the main interface If there are extra cardiac activity this can affect the segmentation e Manually select short axis slices for the LV segmentation This is done by select the slices in question for the segmentation by using the icon A find in the lower right panel in the main interface e Manually point out the center point of the left ventricle Use the icon find in the lower right panel in the main interface and place two points in the middle of the left ventricle in two different image slices The program then adjust a center point line through all slices by ad justing a straight line to these two center points It is important that it is just two points because otherwise the segmentation algorithm ignores them and automatically select center point e Manually change the finished segmenta
164. under pharmacological stress with dipyridamole assessment using T 2 and T1 measurements Magn Reson Med 41 4 686 95 1999 L J Anderson S Holden B Davis E Prescott C C Charrier N H Bunce D N Firmin B Wonke J Porter J M Walker and D J Pennell Cardiovascular T2 star T2 magnetic resonance for the early diagnosis of myocardial iron overload Eur Heart J 22 23 2171 9 2001 D R Messroghli A Rudolph H Abdel Aty R Wassmuth T Kuhne R Dietz and J Schulz Menger An open source software tool for the generation of relaxation time maps in magnetic resonance imaging BMC Med Imaging 10 1 16 2010 H Soneson Strain in the normal human heart assessed by velocity en coded MRI Master s thesis Lund University Centre for Mathematical Sciences 2007 E Bergvall E Hedstrom K M Bloch H Arheden and G Sparr Spline based cardiac motion tracking using velocity encoded magnetic resonance imaging IEEE Trans Med Imaging 27 8 1045 53 2008 BIBLIOGRAPHY 16 17 18 19 20 21 22 23 24 E Heiberg H Soneson E Bergvall K Steding and H Arheden Normal values for strain calculated from velocity encoded MRI In Eleventh Annual SCMR Scientific Sessions 2008 H Soneson E Heiberg E Bergvall E Hedstrom and H Arheden Strain analysis using magnetic resonance imaging can independently identift af fected vessel after acute coronary syndrome In Eleventh Annual S
165. up menu Note that this operation is undoable It is possible to Clear All Annotation Points Clear Annotation Points Using Tem plate Rename Annotations Using Template and Export All Annotation Points When deleting or renaming using a template you are prompted for a tem plate The template must be an exact match since no wildcards are allowed To propagate the location of a time resolved point press Ctr1 F Note that you need to have the annotation tool active when doing this 91 20 Utilities The functions described in this chapter is in US only for off label use and for investigational use The differentiation between a utility and a function feature is that the utility does not necessary apply to an image stack Currently there are five utilities available 20 1 Anonymize DICOM files Recursively This function ask for a folder of DICOM files and replaces the patient name with a new name for all the DICOM files Caution since it overwrites the existing DICOM files and it is recommended to backup these files prior to running this function The function change PatientName and removes patientID DateofBirth OtherPatientIDs EthinicGroup Occupation Additional PatientHistory PatientComments InstitutionAddress and InstitutionName 20 2 Anonymize mat files Recursively This function takes a folder of mat files and anonymize the files and change the patient name to the filename of the mat file This function is particul
166. urrently the use of meta DICOM files is not supported the DICOMDIR file is simply ignored 9 1 2 Loading SPECT DICOM files When loading SPECT DICOM files Segment assumes that the files are re constructed into a short axis stack 9 1 3 General loading DICOM files You can either load each image series at a time or use a graphical tool to select what image stacks to load The graphical series selector is described in Section 9 1 6 To load on image series at a time start by selecting one folder To go up one directory level double click on or click on the icon To more easily get to a different folder click on the Browse pushbutton To go down one directory level double click on the folder name Once selected one folder containing DICOM files a preview of one file in that folder is shown To load the complete image stack perform the following steps 27 CHAPTER 9 LOADING IMAGE STACKS e Start by selecting the imaging technique in the top left corner of the GUI The imaging technique sets the default segmentation parameters and it is crucial that you select the correct imaging technique For many scanners and sequence types this is identified automatically e When a valid file folder is selected a preview of that dataset is dis played Patient details and acquisition time are also shown e It is recommended but generally not required to select Image Type and Image View Plane This tells Segment what kind of
167. use the up down arrows on the keyboard The right image panel a so called m mode image is shown the term comes from ultrasound motion mode This is a resampling of the left image along the white line over time The resampling line can be moved and angled by left clicking on the blue circles and dragging the mouse while the left mouse button is hold down Along the lines there are two callipers shown as a white cross The same callipers are showed in the right image as vertical white dotted lines Distance between 38 10 5 M MODE VIEW Figure 11 Screen shot of the program showing an image stack in M mode viewing mode 39 CHAPTER 10 PROGRAM OVERVIEW the two callipers is displayed under the m mode image To measure time events two time bars are shown in the m mode image These can be dragged with the mouse and the time between them is shown above the m mode image This viewing mode can also be used to make measurements An example on how this can be used is given in Section 12 1 2 10 6 Viewing velocity encoded image stacks For velocity encoded images it is possible to view both the magnitude image and the corresponding velocity encoded image s In the thumbnails a white box is drawn around magnitude and phase image to indicate what image stacks belong to each other For more details see Chapter 23 Flow Analysis 10 7 Playing images as a cine loop In the main icon toolbar the ALAE NIE t 2 controls what time f
168. ustration of this a pink line is also shown in the weighted mode An example of this is illustraded in Figure This line graphically represent the corresponding non weighted area Please note that this line is only provided for visual feed back and should not be used for any quantification purposes The weighted scar delineation method is extensively validated in animals computer phantoms and 40 patients on images acquired both on Siemens and Philips MRI scanners The first step to do viability analysis of delayed enhancement MRI DE MRI images is to delineate both endo and epicardium This can be done either manually or by a semiautomated method In many cases however it may be faster to manually draw the endo and epicardial contours Then select Auto Delineate Viability Weighted method to delineate infarct The automated delineated infarct is now shown with a yellow contour After the delineation you can select the mode of operation The default mode to use is the weighted automatic scar delineation see below for details In the Viability menu you can select mode of operation reset all scar delin eation reset user corrections control visibility and automatic parameters It is possible to add infarct regions by using the pen tool and remove infarcts with the rubber tool 4 regardless of the mode of scar delineation The tool 4 removes the manual corrections made with the Lor 4 By default manually added scar regions shows up in green an
169. vature i e the algorithm favours object with low local curvature The expansion or contraction is allowed to continue for a number of iterations The key to the sucess of the algorithm lies in adjusting an appropriate expansion speed 15 2 2 Optimizing expansion speed Before adjusting the expansion speed you should draw some seed points Im age intensity for the seed points are used in the calculation of the expansion speed image for details see below There is a separate graphical user in terface to help adjusting the speed image calculation This user interface is shown in Figure In the upper left panel an intensity histogram of the complete volume is shown In the lower left panel a function that maps signal intensity to local expansion speed is shown In the upper right image panel a magnitude slice is shown Different slices can be selected by usage of the Slice slider In the lower right image panel the corresponding speed image is shown Bright red and yellow colors denote expansion whereas dark and blue colors denote contraction Four different speed mapping modes can be chosen Gaussian Positive slope Negative slope and Prototype shaped The Gaussian shape is useful when one want to delineate objects within a certain signal intensity range One example is mapping certain Hounsfield units from CT images In future versions of Segment it will be possible to store a set of speed mappings and couple them to the normalized image values
170. ve one bar labelled Start and one labelled End These are used to set the start and end points of motion correction They also affect use of the playback functionality which can be done one image at a time using the playback panel with buttons 41 I and F or making Stress and Rest images play synchronously by using the Play all button 165 CHAPTER 36 PERFUSION ANALYSIS LGE St En St 4 Son Rotate i i 0 10 20 30 40 50 0 10 20 30 40 50 60 0 10 20 30 40 50 60 Contour Stress Sector drvisior a Rest Figure 63 GUI for perfusion analysis 166 36 1 MODULE OVERVIEW Once an interval has been set using the Start and End bars and all slices of one timeframe have been outlined in both Stress and Rest image stacks hit the Motion correction button to start the automatic motion correction This pro cess can take several minutes The result is shown in Figure If intensity from the right ventricle or elsewhere spills into the myocardium segmentation as a result of the motion correction the contour of the respective image stack can be adjusted contraction percentages in the Inner and Outer textboxes and using the Contract Contour pushbuttons labelled Stress and Rest Stress Rest Cine LGE 08 Y Show bloodpoo o 10 15 20 25 30 35 40 45 50 55 Basalanterior Smoothen curve 4f J gt Cont
171. wall motion and infarct parameters The last icon A starts flow analysis tool described in Chapter 47 11 Image settings 11 1 Manually set image description To manually set the image description for an image stack right click on the thumbnail for the image stack Then select Select Image Description in the context menu and define the image description 11 2 Image description upon loading The image description is automatically set in the loading process by compar ing information from the DICOM tags with the information in the text file imagedescription txt You can manually update the text file to improve the automatical definition This is done by open the text file which is found in the folder where Segment is installed Then manually update the text file according to the structure as defined in the first row in the text file and store the text file 49 12 Segmentation of the Left Ventricle Before starting to describe segmentation of the left ventricle it is of impor tance to define what do we consider as the left ventricle 12 1 Definition of the left ventricle At a first thought it seems very easy to define what part of the heart should be included in the left ventricle At a second thought the definition needs to be practical and repeatable In the program the following decisions have been made 12 1 1 Papillary muscles By using the automatic LV segmentation algorithm the papillary muscles are removed as much a
172. y 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 preliminary 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 189 43 Plugi
173. y clicking the Recalculate button The sizes of the core and grayzone volumes are calculated based on pixel volume and displayed in the GUI and can be exported along with the threshold values by clicking the Export button 104 22 Myocardium at Risk Analysis The functions described in this chapter is in US only for off label use and for investigational use The maR tools can be found under the MR menu in Segment The method used for automated delineation of MaR is described by Sjogren et al 9 It uses an Expectation Maximization algorithm to calculate a probability of MaR based on intensity instead of using a threshold and models of the perfu sion territories are used as a priori information to constrain the segmentation The first step to do MaR analysis of T2 weighted MRI T2w MRI images is to delineate both endo and epicardium This can be done either manually or by a semiautomated method In many cases however it may be faster to manually draw the endo and epicardial contours Then select Auto Detect MaR to delineate MaR In the graphical user interface choose the culprit artery in the list box and rotate the yellow line to indicate the inferior inser tion point of the right ventricle and press OK The automated delineation of MaR is now shown with a white contour It is possible to add infarct regions by using the pen tool and remove in farcts with the rubber tool 4 The tool 4
174. y developed algortihm for intro ducing a priori information for a specific application to the level set method used in this tool The prototype holds both spatial information to constrain the segmentation seed points for initialisation of the segmentation and a speed mapping function By the use of a prototype the general segmentation can be made nearly automatic The main idea behind the algorithm is to rather model a constrain of the segmentation stored as a spatial map than to model the object to be segmented For more detailes on the algorithm see 1 A prototype can be generated for a specific application by Medviso AB please contact us at info medviso com to discuss your desired segmentation appli cations To start the prototype based segmentation a couple of landmarks defined in the protoype need to be set by the use of the point tool The landmarks can be set in any of the orthogonal view panels The points shall also be named according to the information in the prototype The specific prototype is chosen in the listbox in the panel Prototype After the selection has been made calculations is done to align the prototype to the landmarks When the calculations are done a light green outline is shown in the orthogonal view panels indicating the startindex of the segmentation which is used as seed points Also the parameters radius curvature and gradient has been set to an optimal value which was stored in the prototype It is possible
175. y plotting the image intensity mapping found under Image tools By 85 CHAPTER 18 REGION OF INTEREST ANALYSIS selecting Multiple threshold analysis numeric the same analysis is performed for each time frame and numeric values are exported to the clipboard 86 ROI Histogram 6 ROIs and 30 timeframes 6 2 a z 2 E 5 z 0 15 0 2 Image Intensity Percentile analysis 0 1 percentile 0 039216 1 percentile 0 066667 2 5 percentile 0 078431 5 percentile 0 082353 25 percentile 0 1098 50 percentile 0 12941 75 percentile 0 14902 95 percentile 0 18824 97 5 percentile 0 20784 99 percentile 0 23529 99 9 percentile 0 29412 Figure 27 Example of ROI histogram 18 7 MULTIPLE THRESHOLD ANALYSIS Threshold visual inspection EIER File Edit Yiew Insert Tools Desktop Window Help Ose 1 49 08 so 10 Levels from 0 1 0 4 Figure 28 Example of multiple threshold analysis 87 19 Measurements and Annotations The whole software package Segment is designed for quantitative analysis and subsequently there are a rich variety of measurement tools available 19 1 Length measurements There are two possibilities to make length measurements The easiest method is to use the measurement tool BA To place a linear measurement left click with the mouse hold mouse button down and drag mouse to the desired location Alternatively or to place a measurement consisting of several line segments hold dow

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