FlowQuant User Manual - University of Ottawa Heart Institute
Contents
1. af 1 Af is y Quick Pick Instructions 1 Select uptake frame using top slider 2 Select transverse slice using side slider 3 Click the LY centre to position the crop box 4 Click Save 159 Target File lc FlowQuantiJOHI_example1 WOHI_example1_restAmmonia_cropped mat FlowQuant User Manual 54 The cropped field can be selected in one of four ways 1 2 3 4 Entering the 6 cropping coordinates directly on the left under Crop The inputs include the starting and ending X Y and Z slices to include in the cropped image By default the original image dimensions are populated Choosing a preset crop under Presets The presets crop the image so that half of the X and half of the Y dimensions and all Z planes are kept The buttons correspond to all combinations of left half L centre half C or right half R and top half T middle half M or bottom half B When any of these buttons are pressed the X Y and Z edit boxes will update to reflect the new cropping coordinates Using Quick Pick Select the desired region by selecting the uptake frame top scroll bar and the transverse slice left scroll bar and clicking on the centre of the LV Tip The uptake frame in which the LV is most clearly defined depends upon the specific tracer The Image Cropper Tool automatically selects the final frame however to facilitate cropping choose the frame with the highest u2. e User Interaction Delay Time sec a setting is available for both batch processing and processing of a single scan The time is specified in seconds enter 0 for no user intervention and infinity inf for mandatory user confirmation e Recycle analysis windows if checked windows are reused rather than created for each new figure This feature is especially useful when batch processing Warning If this feature is not used many windows may be opened leading to poor system respons e Volumetric Viewer selects which viewer the user prefers to use for viewing results Volume Viewer 4D Viewer FlowQuant User Manual 47 e Reports to Save determines which reports to be saved in which image format and to what locations The following report types can be individually configured Orientation includes reorientation LV model uptake polar map and TAC figures Kinetic modeling Analyses Each report can be saved to one or more of the following o Save Local file in the study directory o Print Print to the default local printer o Spool Send to another directory for spooling into an archiving system only tested with Hermes Red text in the spooling directory text box indicates that the specified directory cannot be found Supported file types are png tif or gif o DICOM push as a secondary screen capture to a DICOM complaint PACS system Supported image formats are o File Formats th
3. e Dashed red line metabolite corrected blood activity e Dashed green line the difference between the measured myocardial activity and the fit at that point blue points less the blue solid line i e the residuals In cases where myocardium to blood pool region spillover correction is used the sampled blood TAC is shown with a shaded red line and the spillover corrected blood TAC which is used for the kinetic modeling input function is shown in red FlowQuant User Manual 25 MIE Kinetic Modeling Results File Edit View Insert Tools Desktop Window Help Example_restRubidium_1compDVconst DV 100 Ka 0 51 TEV 0 32 FLOWRC 0 79 1 0 5 f 08 04 ne 8 L 728 s L 8 L 03 0 4 0 1 02 P P P 0 Gradient 8 8 mm mmm UPTAKE 1 2e 005 um FLOW 0 79 Baicc mLimin g mLminig R_SQUARE 0 9 EXIT FLAG 3 BOUNDS 0 Cony Out of Bnds CHI_SQUARE 1 Error 3 1 08 2 06 s E 8 L S LL diter s L 0 4 y 2 P 0 P P P 0 0 High uptake regions K1 0 68 0 01 TBV 0 5 0 013 Blood region s used ABC Activity Bqicc Time minutes Blood spill over correction TBV 0 535 RC 0 665 RC4 TBV 1 b 0 829 FlowQuant User Manual 26 Tip Recycling windows may be important to reduce the chance of exhausting computer resources This can be selected in Study Settings Tip To abort processing close the current window during processing Tip To process a single entry analysis or scan entry right cli
4. A a dada saut 24 le ee ET 24 Single Window Processing in Beta testing 26 PE T RE cade 27 RESUES E Sa 33 FlowQuant User Manual 3 Dynamic Splash Display DSD sense init ais 33 Additional ESTU rer tintin ie AA ead den dre san 36 REMOVING an Entry EE 37 Duplicating an EE 38 Multiple Entry Select iodo 38 VIEWING Data 200 Fac een ti eege een ia Ae 38 TEE TC 41 Settings iCat A a a td 41 Entry Settings rada italie 42 SLU VE le TC 46 General OPINA A Aa 46 O 48 Default Analysis OPTIONS sonera Aa taa deenen 49 Rest Stress Flow Analysis Options iii 49 Making Current Study Settings the Default Settings cocococononoononnnncnnnanonnnnnnnnonananononnnnncnnnos 50 Reverting to the Default Study Setting s 50 Exporting the Study Settings iii 50 Importing Study Settings from another File ccocononooconncnononononannnnnnnnnnnanonononnnnnnnononenonnnnnnonons 50 Kee EE 52 Close AMA tdt 52 Clean Study Directoy cria ten A AA AAA AA AD ta 52 Update Scan Files Directories teed Ge Sede ae a ee as ee ee eeh 52 Image Cropping Tool 53 Motion Correction Tool ssl cias 56 Administrator Tol Sii A nee Re vb EE eee sen nl ent ee 58 FlowQuant User Manual 4 Data Export DynamicData a iaa 59 Data Export KM RESUS iissa nt en eee arte r tine detre See ed eee tt 59 Data Export ROI Coordinates iii 60 Special Considerations for Small Animal PET Image Processing sssssssssssssssessre
5. Making Current Study Settings the Default Settings as explained above Importing Study Settings from another File Select Menu gt Settings gt Load Study Settings FlowQuant User Manual 51 The user may import study settings from either an ini file or from another study This operation overwrites the current study settings FlowQuant User Manual 52 Tools Close All Figures Closes all the FlowQuant generated figures in order to de clutter the screen Clean Study Directory Removes all files from the study directory which are not relevant to the current study settings Update Scan Files Directories This tool is designed to quickly correct the location of multiple image files particularly in large studies which is particularly useful when the directory structure has been reorganized or the study has been copied to another computer When the tool is opened all the existing file locations are listed in the top Select a file location that needs to be corrected and update the location it in the edit box below You may use the browse button to locate the new directory using a directory browser Finally press the Apply to update the location in the current list of directories The directory locations are updated in the study when the OK button is pressed Pressing the Cancel button maintains the current locations in the study File Locations Update Tool 1 Current source directories C Documents and Settings spot
6. User Manual 61 Special Considerations for Small Animal PET Image Processing The previous sections pertained to image processing for scans in humans The process is the same in small animals however special considerations must be made to accommodate their smaller size Select Settings gt Edit Study Settings The default options for each species can be viewed by selecting the species from the Species menu under Default Analysis Options Settings specific to the species and tracer can be obtained by additionally selecting the tracer from the Tracer menu Species specific settings are shown in black text whereas settings common to all species are shown in purple text Although these settings are designed for the specific species they can be adjusted by the user by simply typing in the desired value Image Cropping Tools gt Image Cropping Tool OR Right click the File field of the scan gt Crop File Due to the size of the image files in small animal PET a memory error may result if the user attempts to process the files without using the Image Cropping Tool first General instructions for using this tool are available in the Image Cropping Tools section Gut Cropping During the use of the Reorientation Tool the ellipse is automatically fit to the LV Activity from the liver kidneys is prevalent in small animal PET images and this may interfere with the automatic FlowQuant User Manual 62 ellipse fi
7. attempting to run FlowQuant please ensure that your system meets the minimum requirements listed below In the event that your system does not meet these specifications the proper functioning of the program is not guaranteed by the developer Minimum requirements e Pentium D e AGBof RAM e 10GBof hard drive space available e 1280 x 800 screen resolution e 32 bit colour e Windows XP or Vista operating system Recommended hardware an OpenGL compatible graphics adaptor FlowQuant User Manual 7 Terminology and Acronyms Analysis Entry A single entry comprised of several Scan Entries which contains information required for an analysis between scans and or their analysis results Polar Map PM A 2D rendering of the left ventricle myocardium that enables complete visualization without occlusions Scan Entry A single entry that includes a scan and all of the data required to process that scan Study A list of Analysis Entries that are saved together with accompanying data for future processing and analysis FOV Field of View the spatial region that is sampled by the image GUI Graphical User Interface HLA Horizontal Long Axis KM Kinetic Model LV Left Ventricle Myocardium SA Short Axis TAC Time Activity Curve VLA Vertical Long Axis FlowQuant User Manual 8 Flow Quant Graphical User Interface The FlowQuant GUI shown below is the main interface by which us
8. maps By right clicking on any polar map or 3D surface a context menu with the following viewing options will appear View Polar map View 3D Mesh view a 3D rendering of the polar map with the surface mesh displayed View 3D Surface view a 3D rendering of the polar map with the surface mesh displayed and a softer lighting which gives a smoother appearance View Smoothed 3D Surface view a 3D rendering of the polar map which has been smoothed using the spline points Apply to all PMs in figure apply current view to all other polar maps Copy to separate figure copy the current subplot and its view to a separate figure Volumetric data may be viewed with either VolumeViewer or 4DView For further information please refer to their respective documentations page 47 FlowQuant User Manual 40 FlowQuant User Manual 41 Analysis Settings During the different processing stages certain parameters are used which may be controlled by the user through a hierarchy When a new study is created default study settings are loaded When a new scan or analysis entry is added default entry settings are used The user can modify the scan entry settings analysis entry settings and global settings which are saved as part of the study Settings Hierarchy When processing a study the actual settings for processing are resolved based on a hierarchy as demonstrated in the figure below e Scan Settin
9. motion correction tool is used to determine if the subject moved during a dynamic scan The tool is accessed through the context menu of the image file and brings up the 4D viewer as well as the motion estimation tool which work in conjunction with each other Motion Estimator Tool File Edit View Insert Tools Desktop Window Help Correlation between neighbouring frames r12 Y 2 Blood TAG DER Image Scaling QO User 901 6877 O Global Dynamic Volume Global Selected Volume O Individual Slice Fre E mot Rance 5 0 2 400 0 100 Shift 100 0 100 Shift 4020 02040 0 Shift 5000 Activity Blood TAC Time Activity Gurve 74 82 25 t tt4 t 4 44 Bes a EE HE EH HP 0 8 410 0 10 Shift Enable X Save 40 0 10 Shift M Enable alt fa dal dl Shift Enable Z 5000 Activity Apply Y v Automatically Optimize FlowQuant User Manual 57 The user selects orthogonal x y and z planes on which the analysis is performed by moving the crosshairs to the slices of choice in the 4D Viewer window The motion correction tool is updated with every pixel selected in the viewer The correction tool shows cross correlations between adjacent time frames in all three axes top row as well as on a zoomed scale bottom row In the absence of
10. o Changing speed of playback e Enabling contour lines o Display or hide o Change color e Saving Screenshot or movie FlowQuant User Manual 35 o Screen shot JPEG Printer friendly version White background o Movie GIF or Avi Tra AAA AAA 8 ATP ah To Bo Dee E KK ER Inferior Posterior restRubidium Zoom 56mm Frame 15 Bes mm FremeSpeed AA K ntour On Line Color 2 Frame Sec Contour Off Playback Settings Color Limit Toggles Zoom Slider Frame Slider FlowQuant User Manual 36 Additional Features Many additional features may be accessed through context menus associated with an entry in the study list analysis or scan entry Context menus appear on the screen when the user clicks on an item using the right mouse button The contents of the menus change depending on the object that was Clicked Some entries in the menu are common to the entry analysis or scan and will therefore appear regardless of which part of the entry was clicked Other entries are specific to the field The common context menu entries include Analysis Entry Scan Entry Description Subject Exam Data Physiologic data associated with the exam heart rate blood pressures glucose levels Settings associated with the Process Analysis Settings Process Scan Settings entry Process the entry Process Analysis Overwrite Process Scan Overwri
11. scan is dynamic D gated G or static S This is automatically determined by the image header and can be changed by the user by selecting a different image type Tracer the radio tracer used for imaging automatically determined from the image header State the patient s rest or stress state during acquisition of the image automatically determined from the image header Label a description of the image The list of available labels is determined from the list in the global options and is filtered by the tracer Orientation the study label based on which the LV polar map should be sampled If the orientation is the same as the study tracer label combination of the same scan the LV polar map will be obtained from the same image otherwise the polar map data of another image will be used to sample the polar map The required orientation file is expected to already exist therefore the options available in the pull down relate to the FlowQuant User Manual 16 scan entries above There are three possible ways for this sampling from a previously processed image to proceed as indicated by the lock button that appears to the right of the orientation drop down menu D use orientation to guide sampling lock sampling points ES lock only ellipse size To toggle between the modes simply click on the icon Kinetic Model the kinetic model that will be used to process the image If Default Option is
12. segment with the lowest mean also indicated For an example of the output please see the Flow Defect Quantification figure on the subsequent page The polar map is segmented based on the segment model set in the Study Settings menu The parameter values in each segment are saved in a text file For an explanation of the output values generated in the text file that accompanies the visual output please consult the Rest Stress Defect Analysis Output File Guide as listed in the Additional Documentation section at the end of this manual FlowQuant User Manual 29 Rubidium 1compDVconst Flow Defect Quantification File Edit View Insert Tools Desktop Window Help D d RAR OER Q DE e0 Patient Name Example 28 Sep 2011 Defect Quantification Absolute Scale stressRubidium Flow stressRubidium restRubidium S S E HR 85 0 bpm BP 178 105 mmHg RPP 15100 bpm mmH P VRPP 2 46 P LV LAD LEX RCA LY MBF CYR 2 08 63 5 1 84 704 1174 7421266 459 VMBF adj 2 46 1 E 5412 97 2 16 max 656 59 4 55 4 85 6 max 756 f 91 4 Low Segment mid anterior MBF 1 22 69 6 max Low Segment mid anterior YMBF 1 62 49 8 max restRubidium Flow stressRubidium resiRubidium EI HR 55 0 bpm S BP 112 68 0 mmH RPP 6160 bpm mmHg ARPP 8970 bpm mm adjusted to RPP prFhamHg JD LEX RCA 1 151077 1061 0688 1 141089 1 22 Low Segment mid anterior AMBF 0 4 22 0 max stressRubidium re
13. FlowQuant User Manual Software Version 2 2 4 January 2014 University of Ottawa Heart Institute Cardiac PET Centre 40 Ruskin St Ottawa Ontario K1Y 4W7 Canada 613 761 4275 www ottawaheart ca flowquant ottawaheart ca UNIVERSITY OF OTTAWA HEART INSTITUTE INSTITUT DE CARDIOLOGIE DE L UNIVERSITE D OTTAWA FlowQuant User Manual Disclaimer FlowQuant is protected under international copyright law Use of this software without the sole permission of the University of Ottawa Heart Institute Cardiac PET Centre is illegal FlowQuantO is a research tool that is still in the development phase and is not approved for clinical use Any use of FlowQuant is under the responsibility of the user and the results are not guaranteed by the developer Excel is a registered trademark of Microsoft Corporation FlowQuant User Manual 2 Table of Contents Disclaimer aida 1 Table of Content viii dica 2 INTO Dag E 5 Minimum System Requirements iii 6 Terminology and Acronvms 7 FlowQuant Graphical User Interface ci tia 8 EE 9 Toolbar ste AA nee dl dinars Lun 10 SCY LISTE Rd a A PEA elles see eee tn 11 COMMENTS EE 11 ge IT 11 ROUTING Usina 13 Creating a StU dt ia dad iia 13 Adding an Analysis Entity cid 14 Adding a Scan ENtIyY eocenie enire nesae eae e cil lira 15 Processing a SU asainne koreo ii aii 18 leg e LEE 18 D Medeltge Sampling ii Ra 19 Dynamic Polar2Map EE 23 Blood ROI Processing cuisine
14. G restAmmonia_mismatch80 1 7segment png Database Comparison Allows comparison of rest stress scan pairs to a normal population database Note that this feature is not fully functional at this time FlowQuant User Manual 32 Gated Animation Gated scans are processed in a similar fashion to dynamic scan beginning with the Orientation and PM Sampling stages detailed above LV sampling is then automatically processed for each phase separately A gated report is generated for each scan as shown below The report is gated and cycles through the phases synchronously for all scans Gated Report Study 1 File Edit View Insert Tools Desktop Window Help Zoom 090319_JYHO1_rat2_myoview EF 416473 SV 123 0416 pl LY Volume uL Cardiac Phase Report Date 21 Jul 2009 12 02 00 Capture FlowQuant User Manual 33 During cine playback the user may change the frame rate top right scroll change the zoom on the SA VLA and HLA top left scroll capture the sequence to a movie file bottom left button or pause resume the cine display bottom right button In addition the user may click on the X marks in the volume vs phase curve to select a frame to pause the display on Time frames are always synchronized between all reports Results Images of the results are saved as image files to the study directory the file type can be selected in the Study Settings menu If the option is selected in the Study Settings thes
15. GE scanners No longer required depending on the GE camera model software Save reoriented conical slices turns on an optional saving of an additional intermediate file with the reoriented uptake frames sampled in a spherical conical coordinate system Copy images to study directory copy the image files to the study directory This feature is useful for transferring an entire study to one directory however it increases disk usage Live PM display during LV modeling displays the PM and three orthogonal views for quality control during short axis sampling Process RV enables segmenting and analysis of the RV myocardium in addition to the LV myocardium Color Options Color scheme changes the colour scheme to white grey or black Image Color map changes the color map of the image to either Jet HSV Hot Cool Spring Summer Autumn Winter Gray Bone iBone Copper Pink or HotMetal Polar map Color map changes the color map of the polar maps to either Jet HSV Hot Cool Spring Summer Autumn Winter Gray Bone iBone Copper Pink or HotMetal FlowQuant User Manual 49 Preferred Uptake Units activity Bq cc SUV bw mL g SUV lbm mL g or SUV bmi mL gm Note that SUV values can only be displayed if relevant patient information weight height sex can be retrieved from the scan file header In the absence of relevant data activity units are displayed Default Analysis Options This section p
16. Scan Settings dialogue windows and can also be found under the Default Analysis Options heading in the Study Settings menu The species may be seen on the reorientation reports as well as in the tooltip of the patient name The species can be changed using the species icon to the right of the Patient field FlowQuant User Manual 43 The other sections relate to generating polar maps and the kinetic modeling If the entries are left blank default values will be used from lower levels in the hierarchy Default values if relevant are displayed based on the notation explained in the Default Value Display Feature section in orange under Default Analysis Options The default values are determined by the hierarchy specific for the species and tracer of the scan The editable fields include O Species the species of the patient that was imaged Automatically Determine human dog rat mouse pig e Polar map Options O Plane the transverse plane in the image to use in the first stage of orientation integer value between one and number of planes Gut the last transverse plane in the image to use for the analysis in order to crop out gut liver activity integer value between 1 and number of planes Radial Search 100 200 currently not used Radial sample endo mm the distance from the center of the myocardium to the endocardium Used in conjunction with Radial sample epi A
17. ates the Scan Settings settings for a scan entry Likewise an Analysis Settings dialogue exists for an analysis entry which differs in the scope of influence as dictated by the settings hierarchy explained in the section above Entry settings may be accessed through the context menu of the respective entry Scan Settings SPECIES Automatically Determine Y Polar Map Options Coronary Artery Tree Plane Gut Radial search 100 200 0 Radial sample endo mm 2 LM Radial sample epi mm Anatomy Default __ Ga Brose Type Defaut Y smoothing ent Kernel size 15 Uptake frames E Weighted Sum Detaut Uptake resolution mm 0 20 Normal uptake threshold Segment model lb wv ofrings Kinetic Modeling Options Start time mins End time mins Automatic motion correction Detaut v Blood spillover correction betat Ml Auto estimate RC Defaut Recovery coefficient 0 1 DY K1 2 Retention integra Use default O Peak ti 14 0 2 O Time 7 Gamma tit Blood input Default Detaut ei RY blood correction Default M Fast flag Default Restore Defaults The species section in both the Analysis Settings and Scan Settings menus allows the user to override the species that was imaged and may be useful if the wrong species is identified by the software This field is located at the top of the Analysis Settings and
18. cessed sequentially starting with a transverse plane The reorientation tool allows the user to monitor the process as well as manually intervene if required The transverse plane may be modified by sliding the arrow shown in green on the grey slide bar to the left of the Transaxial Plane figure Similarly the gut cropping slice which allows gut liver activity to be cropped from the FOV can be manipulated using the gut bar blue on the same slide bar The plane and gut settings can be preset in the scan settings dialogue or left blank in which case they will be automatically determined at the start of processing each scan Additionally the colour saturation of the image may be modified for better visualization of the myocardium by sliding the green arrow shown on the Colour Saturation slider bar The process begins with completely automated fitting a countdown timer shown in parentheses on the accept button provides the time for the user to intervene Once any change is made the timer stops and the user is no longer limited by time If no changes are made and the time runs out the results are accepted and the LV model fitting LV sampling stage is initiated The user may also click the accept button if no intervention is required The user intervention time may be set in the General Options dialogue of the study settings menu FlowQuant User Manual 19 In each of the three orthogonal planes a partial ellipse is fit to the LV sho
19. ck on the entry and select Process Scan Overwrite or Complete from the context menu Single Window Processing Optionally the user can choose to process a dynamic study using a single window rather than all the figures shown above The same processing steps apply with similar operator interaction No approval is required between steps however and processing continues from point of interaction This option may be turned using the study setting explained below FlowQuant User Manual 27 Quantification using Dynamic Image D ds 1 48 790 2 08 00 Example_restRubidium ID 9603549 Sex Female Height 155cm Weight85kg BMI 35 4 Processed 28 Sep 2011 10 39 39 FQ V2 2 0 Study Type REST RB DYN FBP12mm Tracer Rubidium Modality PT Resolution 12 mm Species Human Acquisition date 19 Aug 2010 14 55 03 Uptake Frames 11 15 8min Image File CAFlowQuantiStudiestExam plelExam ple Resta HeartRate 55 bpm BloodPressure 112 68 mmHg a Transaxial Plane 24 47 mid VLA Position Auto Position Auto aot Angles Auto Angles Auto Size Auto Size Auto E 3 a Za A cio A a ER Orientation from Current study SNR 11 8897 MER 2 0178 A MB 49 58 i mid HLA basal SA Position Auto Angles Auto Size Fixed 08 S Left Lateral Vi 3 08 D lew H Se a zos D LES 02 S SA angle 0 preset Ge E preci men
20. different mismatch options Normalize whole LV this is the standard option LBBB exclude septal half LV to be used in cases of left bundle branch block where it is not useful to include the septal half LV in the analysis LBBB exclude septal wall to be used in cases of left bundle branch block where it is not useful to include the septal wall in the analysis LBBB lateral wall only to be used in cases of left bundle branch block where it is only useful to include the lateral wall in the analysis DBM no FDG normalization to be used in cases of diabetes mellitus where FDG normalization is not useful Normalize whole LV using K1 map use the K1 map for the perfusion tracer rather than the uptake map FlowQuant User Manual 31 Mismatch Analysis File Edit View Insert Tools Desktop Window Help DNS RARV E 08 50 Date Generated 05 Oct 2010 16 rings 17 segments Patient Name UOHIexample1 rest mmonia restEDG LY BO 100 LY 25 L P P rest mmonia defect restFDG defect norm iged nor lized DN P P Match Mismatch L Reverse bn raw Reverse Mm norm restAmmon ef Ost DG rest mm ia pERstEDG E rest mmonia d egt Mismatch cw i P Normal threshold 80 Match Mismatch rest mmonia defect checksum 100 Directory CiFlowQuantiStudieslUOHI_example1 Text file UOHlexample1_restFDG restAmmonia_mismatch80 1 7segment tt Graphic file UOHlexample1_restFD
21. e FlowQuant User Manual 38 Confirm the removal by clicking on the Yes button in the confirmation pop up box Duplicating an Entry Select the entry gt Click on the duplicate button in the toolbar OR gt Right click on the entry and select Duplicate from the context menu The duplicated entry is entered at the bottom of the study list for an analysis entry or at the bottom of the analysis list for a duplicated scan entry Multiple Entry Selection Hold the Control Ctrl key gt Click on the entry entries of interest gt Release key when done This function is useful for removing duplicating processing and changing the settings of several entries at once Note Multiple entries do not currently support result viewing Note Only entries of the same type i e analysis or scan can be selected simultaneously to avoid ambiguity Viewing Data In a scan or analysis context menu under View Results several of the datasets may be viewed These include Header Dynamic Image FlowQuant User Manual 39 Uptake Image Smoothed Uptake Image PM Sampling PM Sampling Validation Tool Reoriented Image Smoothed Reoriented Image Dynamic Image Splash Uptake PM Dynamic Sequence Viewer Dynamic Sequence Report KM Data blood time activity curves and dynamic polar maps KM Results Gated Results Context menus also exist for 3D surface viewing of polar
22. e file formats which the reports will be saved in include Matlab Figure fig Post Script eps Enhanced Metafile emf Portable Network Graphics png TIFF Compressed Image tif Print to default printer Note this option may be convenient in some cases but may also lead to excess waste of printer supplies Gated Report mpeg Gated reports can only be saved as animated gif files to the local study directory This section includes options that are specific to the type of study and includes the following options e Scan Labels List a list of possible labels that are available in the label pull downs of each scan entry The list should be edited to reflect the nature of the study They should typically follow the format descriptionTracer where the description may include rest stress baseline follow up 240s infusion etc Below are some examples Example study Example labels FlowQuant User Manual 48 Comparison of perfusion with Rubidium and RestRubidium Ammonia StressRubidium RestAmmonia StressAmmonia Clinical use with Rubidium and FDG mismatch RestRubidium analysis StressRubidium RestFDG StressFDG The tracer section will be used to help resolve the relevant labels to each entry based on the tracer in the image information Apply scatter fraction correction enable disable correction for scatter fraction if need be specific for Rb scans on
23. e results may also be printed to the default printer Reports can be saved to an additional directory by checking Enable spooling in the Study Settings dialogue Dynamic Splash Display DSD Dynamic Splash Display is an interactive GUI that provides the user tools to visualize processed studies DSD is intended to interpret rest and stress perfusion studies but is compatible with dynamic gated and static images providing more advanced functionality Studies can be of the same or different patients or baseline vs follow up DSD allows the user to also view CT images of the same patient fused with emission images If dynamic images are present the user has the ability to play trough the image sequence and view time activity curves Screen captures can be saved as movie or still images Movies can be saved in gif or avi format while images are saved in JPEG format The header at the top of the figure contains relevant patient data e g patient identifiers patient age patient weight blood pressure heart rate A series of buttons controlling majority of the features are located at the bottom of the figure The buttons control everything from the colormap being displayed to the zoom of the image By default the DSD shows select slices through the LV and the toggles located above each image can be used to scroll through the slices being displayed and to align between image series Similarly the frame slider toggle at the bottom of
24. ers interact with the program This GUI provides the means to setup a study list process the study and view its results r 1 Tracer_ e Le S Rubidium est restRubidium Y restRubidium restFDG restFDG v Patlak Analysis Species Icon Settings unlocked Scan Entry Tracer red signifies a difference Analysis Entry from the filename Study List scrollbar Process Buttons ER FlowQuant User Manual Menu The menu system contains all functionality pertaining to study files settings as well as various analysis tools The menu includes the following hierarchy and shortcut key combinations in parentheses e File o Load Study CTRL O o Save Study CTRL S o Save Study As CTRL A o Clear Study o Add Analysis Entry CTRL N o Add Scan Entry CTRL E o View Study Directory o Exit CTRL X e Settings o Edit Study Settings CTRL P o Save Current Study Settings as Default o Load My Default Study Settings o Save Study Settings o Load Study Settings o Load Factory Settings o Close all figures CTRL F o Clean Study Directory o Update Scan File Directories o Image Cropper o DICOM Conversion Server FlowQuant User Manual 10 Data Toolbar The toolbar contains quick access to a subset of functionality from the menu that is most commonly used Administrator Tools Export Dynamic Data Export KM Results Export ROI coordinates Help Check for Updates About New S
25. ert Tools Desktop Window Help G FlowQuant Studies Example Example_restR ubidiurn_PMsampling 3D Surface Left Lateral View Polar Map sd 0 Activity Bq cc Anterior View Posterior View Ant Ant FlowQuant User Manual 23 A drop down menu appears in the Registered Polar map window which gives the option of viewing the 3D polar maps as a 3D Surface default Smoothed 3D Surface or 3D Mesh Dynamic Polar Map The orientation and sampling are then applied to all time frames of the image sequence This generates a dynamic polar map as well as blood time activity curves Three blood time activity curves are sampled left ventricle cavity left ventricle base and left atrium A TAC figure is created with the three blood TACs their median and their mean myocardial polar map as shown on the PM TAC Time Activity Curves File Edit View Insert Tools Desktop Window Help Example Rest gt Example_restRubidium_dynamicData Possibi patient motion detected cavity E base atrium Blood median Blood pool ROI Myocardium Motion Gutoff Shift px o g o a 160 2 lt Time min FlowQuant User Manual 24 A gamma variate model is also fit to the Blood Media TAC and the model parameters are displayed in red for reference During this stage motion detection takes place If motion correction is turned on correction is also applied The small shift graph re
26. ertains to default values for analysis Note that the fields in this section are similar to those in the process scan analysis settings dialogue The description of each field in this panel is explained in the Entry Settings section above The user may select combinations of species and tracer and general default and default values for different species using the two pull down menus at the top of the panel Default values which are determined through the hierarchy are displayed using the notation as explained below Element Default User Defined Edit Boxes Blue text Black text Shown in tooltip while Pull Down Menus hovering cursor over pull down menu Radio Buttons Bold text Regular text Rest Stress Flow Analysis Options These options control processing and reporting of Rest Stress Analyses Options include Normal Rate Pressure Product RPP rate pressure product to which rest perfusion scans are normalized for RPP correction Normalize only if RPP is greater optionally applies normalization of flow to normal RPP if RPP is greater than the normal RPP Otherwise normalization will be applied regardless if RPP is greater than or less than normal RPP Defect Clinical Classification Method determines the classification scheme by which flow segments are classifies Gould based on Nils P Johnson Lance Gould Integrating noninvasive absolute flow coronary flow reserve and ischemic th
27. ftware FlowQuant User Manual 46 Study Settings The Study Settings dialogue is shown below The study settings are split into General Options Study Options and Default Analysis Options Study Settings ES x General Options Study Options User Interaction Delay Time SH Scan Labels List Single entry processing inf rest PDG Al a restAmmonia A Batch processing 20 stressAmmonia restRubidium ds O none inf indefinate stressRubidium restFlurpiridaz Single window for scan processing stressFlurpiridaz restSestamibi M Recycle analysis windows stressSestamibi e __ restAcetate Volumetric Viewer 14D Viewer M stressAcetate restHED Reports to Save SCT stressHED a Save Print Spool DICOM Delissen Orientation M Apply bias correction Kinetic Model v Save reoriented conical slices RES S Copy i to study direct a opy images to study directory Save Formats v Live PM display during LW modelling ST Process RV Matlab Figure fig Post Script eps color options Enhanced Metafile emf Color Scheme Bitmap White M Text Portable Network Graphic png Image Colormap TIFF Com ed Image tif Dies ey Done j E Spooling Polarmap Colormap C dicom_spool Bro
28. further analysis of the kinetic modeling results by exporting the desired data into an Excel spreadsheet The user is queried where to save the results and is then queried for the FlowQuant User Manual 60 desired parameters to record and into how many segments the polar map should be divided The user may specify how many rings of the polar map to use or let FlowQuant automatically determine An operation to perform on all pixels in a segment is also required e g Mean Median Standard Deviation Standard Error Maximum Minimum KM Results Export C Uptake _ Net Uptake ki Oka O Flow Jpc C Flowrc O kz ld O k3 Clk4 Number of Segments 3 ASNC M Number of Rings DT PATLAK slope Auto v Oretenti Segment Summary Opeartion ention Mean v C RMS Error A new sheet will be created with the results tabulated with each parameter of each segment ina column and each scan in a row Only the available results images that have been processed are tabulated Parameters that are not part of an entry s kinetic model are left empty The order of the entries is as specified in the study list Data Export ROI Coordinates This tool exports the ROI coordinates from the SA sampling phase of the processing to a CSV file This is useful for importing the desired region of interest into other software packages for further or comparative analysis using the same initial registration of the data FlowQuant
29. g Highest most specific e Analysis Setting e Study Setting o Species Tracer Lowest least specific Scan settings are specific for a scan entry and therefore are top priority Settings that are common to all scan entries in an analysis entry may be set through the analysis entry settings However if conflicting entries exist between analysis and scan entries the scan setting will always prevail as dictated by the hierarchy Study settings are split into combinations of species and tracer Thus the user can specify different default settings for species tracer combinations The hierarchy dictates that settings that are species tracer specific have higher priority than settings of the species alone At the lowest level of the hierarchy are default settings that are not specific to any species or tracer If settings global analysis and scan are left empty default values will take effect which are determined by working backwards through the hierarchy Therefore if a setting is not specified for a scan the analysis setting will be used If that hasn t been specified either the study setting for that species tracer combination is used If that is set to default the species setting is used Finally if the species setting is set to default the software default setting is used The entire global settings can be edited using the global settings dialogues FlowQuant User Manual 42 Entry Settings The following image demonstr
30. he center of the myocardium The reoriented image is re sliced in a bottle brush fashion to generate a sequence of slice images with a circular pattern A spline model with 13 degrees of freedom is then fit to the image The Short Axis Rotational Control an additional sampling point line exterior to the septal wall is present on a single slice image This line indicates the center of the septal wall and is included to ensure that the septum is displayed in the common orientation on the polar map i e centered on the left side of the polar map Manual adjustment varies the short axis angle from 0 as shown in the bottom right corner of the window The figure on the following page demonstrates the slices from apex to atrium top left to bottom right Similarly the horizontal and vertical long axis slices are displayed The fitted model is displayed as a red line except in the horizontal long axis where it is cyan In the short axis slices the epicardium and endocardium are also drawn in solid red lines FlowQuant User Manual 20 EI Reorientation Tool File Edit View Insert Tools Desktop Window Help E Position Auto Position Auto Angles Auto Size Auto Species Human NL a k SNA 11 6637 BR 2 0176 Position Auto le Example RestA pe REST RB DYN FBP12mm a es date 19 Aug 2010 14 55 08 Bon ana processed 28 Sep 2011 10 03 04 A countdown timer as in the Reorientation Tool exists providing time for
31. ies directory see Administrator Tools for more detail When the file is saved a subdirectory with the same name will be saved in the same directory The study file contains all of the data required by FlowQuant and the directory contains all of the result files Several menu options and toolbar buttons relate to the study New Study clears the existing study from FlowQuant Load Study loads a previously saved study file into FlowQuant Save Study saves the current study If the study has not yet been saved the user is queried for a study name and a directory in which to save it Save Study As saves the current study under a new name and or directory without removing the original study and corresponding results files If a new study has been created and processed before saving the user is first queried for a study name and directory in which it will be saved Tip Use descriptive file names and organized directory structuring that will enable you to locate a study even in the distant future Tip If a single patient is being processed for example for a clinical case consider saving the study in the directory with the original patient data FlowQuant User Manual 14 Adding an Analysis Entry An analysis entry may be added either through the menu or the button on the GUI When this option is selected a new dialogue window opens enabling the selection of a single scan or multiple scans to be added fro
32. ll automatically update the image Tip The playback feature in the 4D Viewer may be used in conjunction with the motion estimation tool to evaluate image motion FlowQuant User Manual 58 4 When satisfied with the correction press the Save button to save the image to a new file The new filename will automatically replace the existing one in the scan entry The motion correction can be cancelled by closing both windows Administrator Tools The administrator tool provides additional advanced options that are intended only for a user overseeing the FlowQuant installation The administrator tool is password protected with the default password set to password but the user may choose to change the password after receiving administrator access The administrator tool can be used to configure default directories for study and scan file locations and tracer and state dictionaries can be edited Administr EI password Advanced FlowQuant Options Default Studies Directory C FlowQuant Studies Default Scan Files Ic Scans Lets the administrator specify how tracer strings are translated into fixed notation Edit Tracer Dictionary Edit State Dictionary Let the administrator specify how state strings are translated into fixed terms Administrator Password Password password Unchanged Retype Password password FlowQuant User Manual 59 Dictionaries are used to config
33. m an accessible directory A new analysis entry is added at the bottom of the study list In the Analysis field the user may choose an analysis type from the pull down menu UO exemple M LOH_exampiet M CFlowQuertUOHl_exa OD OG OS Acetate v rest cetate Y restAcetate wl Acetate One Co w ert OH exs QD OG OS Acetate EI rasticetate Y lrestacet e ml Acetate One Co M On Rest Stress v This analysis entry contains 2 scan entries FlowQuant automatically determines the type of analysis based on the type of scans that were selected Rest Stress Analysis if one rest and one stress scan were selected For this particular study type a special dialogue is displayed to enter heart rate and blood pressure data Example Rest Stress Exam A Blood Pressure Heart Rate Systolic Diastolic ee m2 i e 85 178 1 hos bpm mmHg Yalues can be either scalars or a series seperated by spaces or commas The mean will be used Mismatch Normalized whole LV analysis if one metabolic FDG or acetate and one perfusion Rb or ammonia scans were selected Each analysis entry has analysis settings that may be edited by the user By default these settings are left blank reverting to the study settings as described in the Settings Hierarchy section on page 23 The analysis entry settings may be accessed by right clicking on the desired analysis entry and selecting Process Analysis Setting
34. ove the current entry analysis entry or scan entry highlighted in green up in the study list e Down arrow move the current entry analysis entry or scan entry highlighted in green down in the study list e Process Buttons process the study list in order from top to bottom Four button combinations exist o Complete Files All process all of the study list steps that have not yet been processed Existing files are used if they are valid otherwise they are overwritten This is useful for quick completion of only the missing data FlowQuant User Manual 12 Complete Files Selection process the entries that are selected by the checkbox Existing files are used if they are valid otherwise they are overwritten Overwrite Files All process the entire study list without regard for existing files Existing files will be overwritten resulting in a longer processing time Overwrite Files Selection process the entries that are selected by the checkbox without regard for existing files Existing files will be overwritten resulting in a longer processing time FlowQuant User Manual 13 Routine Use Creating a Study A study is created when it is first saved and it must be created for processing to take place This is due to the need to save result files during processing The study file named with a std extension can be saved to any directory but by default will be saved to the C FlowQuant Stud
35. patient motion the darkest red regions would align on the zero shift line The tools can be used together as follows 1 Select the pixel as well as time frame in the 4D Viewer window 2 Control points marked by symbols are superimposed on the zoomed views The user can interact with the control points to correct motion by clicking and dragging each point If there is no motion in the image best cross correlations red will run as centered vertical lines in all three axes In practice some small deviations may be expected The control points should superimpose the cross correlations closest to unity red Select the highest correlation dark red with the control points This can be done in two ways i Manually adjusting each control point by clicking and dragging them to the darkest red regions for the X Y and or Z axes Select the axes to optimize along by checking Enable X Enable Y and or Enable Z below each zoomed frame in the Motion Estimator window ii Using the Automatically Optimize button Select the time frame to optimize by clicking and dragging the horizontal black line to the desired time frame The optimization will apply to all frames below this line Select the axes to optimize along by checking Enable X Enable Y and or Enable Z below each zoomed frame in the Motion Estimator window Click Automatically Optimize 3 Click Apply and the Motion Estimator and 4D Viewer windows wi
36. presents motion in x septal lateral y anterior posterior and z apex base direction in mm The vertical black line on both the motion and TAC curves represents the cutoff frame for which motion detection was applied right of the line Blood ROI Processing This processing step happens in the background A blood pool frame is automatically selected based on the blood TACs and the image is used to automatically define a blood ROI which may be used as a blood input function to the kinetic model stage in place of the previously discussed regions ABC The LV model figure is also updated with the blood ROI shown as a red patch Kinetic Modeling The last stage of processing a scan includes running of the kinetic model Description of all kinetic models is beyond the scope of this document but they all result in a similar figure format A series of polar maps are displayed for the uptake kinetic model free variables chi square r square exit flag and upper bound saturation At the bottom half fitting information for the selected sector is displayed By default the mean of the high uptake regions is displayed but the user can click on any sector of the polar map to view its specific fitting data The fitting graph shows the following activity curves e Blue points measured myocardial activity e Solid blue line the model fit to the measured myocardial activity e Cyan line pure myocardial signal e Solid red line measured blood activity
37. ptake before selecting the transverse slice Using the Volume Viewer tool A range of frames to view may be specified in the edit box By default only the last time frame is selected If the images are large selecting too many frames may lead to out of memory errors Once the desired time frame range has been selected click the Use Volume Viewer button The Volume Viewer enables the specification of cropping ranges by the moveable green and red bars on the axis rulers Accept results by clicking on the Acquire Volume button The A link to the Volume Viewer documentation is found on page 42 FlowQuant User Manual 55 selected cropping coordinates will be displayed in the coordinate edit boxes mentioned in option 1 volViewer File Controls Slice Defaults All Slices Help UEFA ii ODO Colormap CETTE l Sum or Range eg et e ann me X Axis By default the target file will have the same name as the source file with_ cropped appended to the end of the filename The file will also be saved as a mat file Click the save button to save the cropped image If the Image Cropping Tool was accessed through a context menu the file entry will be populated with the cropped image file name FlowQuant User Manual 56 Motion Correction Tool Tip As of version 2 2 0 automatic motion correction can be applied to dynamic images The motion correction tool described below is a manual correction The
38. resholds into a comprehensive map of physiological severity JACC 2012 5 4 430 440 Ottawa unpublished Prior unpublished FlowQuant User Manual 50 Apply RPP controls if classification is performed using RPP corrected or uncorrected reserve values Confidence intervals optionally display confidence intervals around classification points Intervals can be specified for CFR and stress flow individually either as of value or in absolute units Generate Summary Report optionally generates a summary clinical flow reserve classification report based on the either Flow or FlowRC values Making Current Study Settings the Default Settings Select Menu gt Settings gt Save Current Study Settings as Default This will set the default study settings for future studies Reverting to the Default Study Settings Select Menu gt Settings gt Load My Default Study Settings The user may load the default study settings to override the current study settings The user is prompted to confirm the operation as the current settings will be lost Exporting the Study Settings Select Menu gt Settings gt Save Study Settings The user may export the current study settings to a file The user is prompted for a file name and location The ini file is saved and may be imported in the future Note The MMSettings ini file in the FlowQuant directory is the default study settings file Saving to this file is equivalent to
39. s If the settings are not all empty i e if the user has entered FlowQuant User Manual 15 values that are different from the default study settings a red exclamation mark will appear to the left of the analysis entry once the OK button has been selected and the Analysis Settings menu closes Adding a Scan Entry Using either the button on the GUI or the menu the user may add a scan entry into the currently selected analysis highlighted in green The user will be queried for an image file Once the file is selected the scan analysis entry fields will be automatically populated based on the file header which must have been saved to the same directory as the image file Ensure that the right tracer and state have been determined Patient Tracer State Label Orientation Kinetic Model UOHI_examplet 14 C FlowQuantiJOHI_examp b Oc Os ammonia w Rest restAmmonia rest mmonia v Ammonia One Co v The scan entry fields are as follows Patient a unique name for the individual By default this will be the patient name If the mouse cursor is placed over the field a tool tip with the species is displayed for user confirmation The species is also indicated by the icon to the right of the patient entry field This can be changed by right clicking on the icon and selecting a different species File the location of the file containing the image data Image Type indicates whether the
40. s d Senna Motion Detection e ZER Model rubidium_1compDVconst with DV 100 ay E gt e D 10 ni A i i A R A UPTAKE 1 3e 004 FLOW 0 79 K1 0 51 TBV 0 32 2 a D 8 10 12 14 Frames f x 10 High uptake regions CS S L s L 3 s00 Ki 0 52 0 01 25 4 gt TBV 0 33 0 013 P o p d e der A Bafoo fe Gradient 12 ring E Blood region s used ABC 1 1 6 1 CHILSQUARE 1 R_SQUARE 0 9 EXIT_FLAG 3 BOUNDS 0 3 d d Conv Out of Ends 1 os 0 5 E 0 8 s L s L s L f dier s L D i 0 4 0 1 2 3 4 5 6 7 Time minutes Blood spill over correction TBV 0 595 RO 0 665 ROHTBV 1 b 0 629 P E P b P PE P in Range Analysis Upon completion of the scan entry processing the analysis selected in the Analysis drop down list will proceed There are four main types of analysis available e Rest Stress e Mismatch e Database Comparison not yet fully activated e Gated Animation Rest Stress This analysis method provides rest stress reserve stress rest difference stress rest and stress rest gt threshold where threshold is the value set by the user in the Study Settings menu values lt threshold are considered to be defects polar maps for each of the relevant parameters FlowQuant User Manual 28 from the kinetic model processing For example for the 1 compartment DV model polar maps for uptake DV K1 and flow are presented Below each polar map the mean and of maximum are given for each major coronary territory and the
41. selected the model is chosen based on the tracer and the species of the subject If None is chosen kinetic modeling will not proceed Each scan entry has settings that may be edited by the user By default these settings are left blank reverting to the study settings as described in the Settings Hierarchy on page 23 The scan entry settings described in Scan Entries page 23 may be accessed by right clicking on the scan entry and selecting Process Scan Settings If the settings are not all empty i e if the user has entered values that are different from the default study settings a red exclamation mark will appear on the scan entry once the OK button has been selected and the Scan Settings menu closes Likewise the Subject Exam Data including heart rate blood pressures glucose levels and tracer specific activity can be edited The Table below lists how these parameters are used FlowQuant User Manual 17 JANE DOE restFDG Exam Data Hemodynamics Heart Rate Systolic Diastolic Glucose Yalues Specific Actitvity E 150 r 110 bpm mmHg mmol L GBq umol Tracer Activity Patient Weight Patient Height Injected Activity Before Injection at Kg meters Scan Time 15 15 42 Residual be at Time HH MM SS CTAC image file i Erowse Values can be either scalars or a series seperated by spaces or commas Parameter Units Usage Hear
42. sressssrsereesrssssesereese 61 Additional Documentation tdi 63 FlowQuant User Manual 5 Introduction FlowQuant is developed by the University of Ottawa Heart Institute Cardiac PET Centre Originally FlowQuant was intended as a tool for quantification of physiological function from dynamic positron emission tomography PET However additional tools and analyses are continuously being added to support static and gated imaging of nuclear imaging modalities Flow0QuantO is a menu based GUI which is able to process large sets of scans both in a research and clinical setting Typical processing of dynamic images includes the following steps 1 Scan processing a Generating polar maps uptake and dynamic sequence and sampling the LV blood pool time activity curve TAC b Kinetic modeling using the dynamic polar map and blood TAC 2 Analysis of the results of sets of scans This includes mismatch analysis and rest stress comparison This document provides information on using the FlowQuant tool and its features More specific information about sampling polar maps kinetic models and analysis tools is published in literature The goal of this document is to form a user manual not to describe the science It is therefore expected that the reader has sufficient background in nuclear cardiac imaging and be current with the field of quantitative imaging FlowQuant User Manual 6 Minimum System Requirements Before
43. stRubidium gt threshold e oo EX Number of rings 16 2 69 Nah 000 2 02 304 Defect threshold is absolute Flow 75 of max values are Flow emax 720 00 51 6 SE Low Segment mid anterior mean 1 23 S 5 max Output path C FlowQuantiStudies Example Output file Example_restRubidium stressRubidium_1compDVconst_FlowDefect 5 Values 17segment txt FlowQuant User Manual 30 Mismatch This analysis method provides a comparison between the uptake of the perfusion tracer and a viability tracer for example N 13 ammonia and FDG Polar maps of uptake defect area area lt threshold normalized to the maximum value of the LV match perfusion defect mismatch mismatch FDG perfusion reverse mismatch raw perfusion FDG reverse mismatch normalized perfusion FDG normalized to maximum of LV are presented Above each polar map the of LV that corresponds to that parameter is indicated For an example of the output please see the Mismatch Analysis figure on the subsequent page The polar map is segmented based on the segment model set in the Study Settings menu The parameter values in each segment are saved in a text file For an explanation of the output values generated in the text file that accompanies the visual output please consult the Mismatch Scores Output File Guide as listed in the Additional Documentation section at the end of this manual Note that there are six
44. t Rate bpm Rate pressure product correction of rest flow values Coronary vascular resistance CVR in stress perfusion scans Systolic Blood Pressure mmHg Rate pressure product correction of rest flow values Diastolic Blood Pressure mmHg Rate pressure product correction of rest flow values Glucose Values Mmol L Measured glucose values used for calculating the MGU values from the Patlak model for FDG scans Once entered the values will be averaged resulting in a single value Specific Activity GBq umol Tracer Concentration nmol cc uptake values Tracer Activity Standard uptake values SUV calculations Patient Weight Kg FlowQuant User Manual 18 Patient Height Meters Activity before injection MBq Residual activity MBq Assay time before injection hr min sec Residual assay time hr min sec CTAC image file Filename CT and emission data fusion in Dynamic Splash Display Processing a Study By clicking on one of the process buttons batch processing of the selection is started from top to bottom of the study list First all of the scans of an analysis entry are processed and then the analysis entry is processed The scan entry processing consists of several steps that follow in sequence Reorientation An uptake image is generated by summing the uptake frames as specified in the uptake field of the scan entry Three orthogonal slices are taken in which the LV is registered The slices are pro
45. te o ie overwriting existing results Process the entry completing only the results Process Analysis Complete Process Scan Complete that have not yet been processed Duplicate Duplicate the entry Remove the entry from the Remove study list View Results View results a sub menu lets the user select the desired result to view Delete Results Delete results a sub menu FlowQuant User Manual 37 lets the user select a set of results to delete Export the blood TAC toa Export Results CSV comma separated variable file Enter heart rate blood Subject Exam Data pressure systolic and diastolic and glucose values Specific context menu entries include Filename View view the raw image View Smoothed view the raw image after it has been smoothed to the resolution specified through the settings hierarchy View Header view the image header information Select File select an image file using a browser Crop File crop out parts of an image that are not relevant to the analysis and may adversely affect software automation Motion Correct File adjust for patient motion Orientation Import Orientation import the orientation from a previously processed file PMSampling mat file Removing an Entry Select the entry gt Press the delete button in the toolbar OR gt Right click on the entry and select Remov
46. teriMy Documents MATLABiHuman 2 Replace source directory with C Documents and Settings spotter My Documents MATLAB Human Directions Use this tool to correct the directories in which your images are located 1 Select the source directory that requires update 2 Type or browse to the correct directory 3 Apply the changes 4 Repeat for any other directories that require correction FlowQuant User Manual 53 Image Cropping Tool The Image Cropping Tool is intended to crop out parts of an image that are not relevant ex a urine pool under the animal uptake in an adjacent organ or irrelevant areas to the analysis and may adversely affect the software automation ex out of memory errors The Image Cropping Tool may either be accessed through the tools menu or by the context menu of a specific image filename entry If the Image Cropping Tool is accessed through the context menu the image filename will already appear as the source filename which will not be editable If the tool is accessed through the menu the source file field will not be populated and the user will have to enter a file Below is an example dialogue accessed from the context menu Image Cropping Tool Source File CAFlowQuantiJOHI_example1 WOHI_example1_restAmmonia v Crol E A Presets 1 4 slices Cropping Tool x 83 4 210 ES SE Y 129 EI 256 H Note Large files may not be viewable with ll fi due t memory restrictions
47. the figure allows the user to change which frame is currently being displayed on the figure if the images are dynamic or gated The Time Activity Curves plotted in the DSD are also interactive By moving the blue bar around the user can change the time frame being displayed If the user drags the bar to cover multiple time frames the images will update to a summation of the time frames FlowQuant User Manual 34 The user also has the ability to view the contour lines on the image by toggling them on and off DSD also allows the user to fuse PET and CT images together for further comparison Using the slider located below the Time Activity Curves the user can select mixing of the CT and emission images By default 100 emission data will be displayed If no CT data is loaded into FlowQuant this slider is not visible A list of addition features in DSD is as follows e Ability to change the color limits of the image o Custom Using a slider or preset values o Study Max and min of the entire data set o Frame Max and min of entire data set within a frame e Changing the colormap o Inverse of colormap e Changing the x and y scale of the TACs o Logarithmic or linear e Settings the Zoom of the Image e Changing the image slices being displayed e Changing the image frame being displayed dynamic gated only e Image Transparency CT data required e Playback of images dynamic gated only o Loop forward o Sweep forward then backwards
48. the user to intervene if need be The user may drag any of the rings in the short axis slices of VLA HLA to manually assist with the fit Each ring in the short axis slices is paired with a ring in the VLA red of the HLA cyan Also if the septal wall sampling point line does not appear to be centered on the septal wall the user may change its orientation by dragging the point line The green circle which is fit to the apex FlowQuant User Manual 21 in the VLA and HLA frames may also be manually adjusted The user may also click the Optimize Fit button to improve the fit using the manual fit as a starting point The Common image scale check box allows the user to swap between independent scaling of each image in the figure for improved contrast and a common scale for all slices Ier LV Model Tool File Edit View Insert Tools Desktop Window Help EI Optimize Fit Accept 1 Common image scale Live Polarmap Display FlowQuant User Manual 22 Once the LV model has been displayed the Registered Polar map a static uptake polar map and model figure is also shown for visualization of the whole LV to ensure proper fitting The model figure is displayed from three different angles to overcome visual occlusion Missing sectors sectors that are outside the FOV are not displayed Once the LV model has been accepted a larger version of this figure is displayed Registered Polar Map EE File Edit View Ins
49. tting polar map and kinetic modeling The Gut Crop slide bar is automatically set at the maximum number of planes no cropping and can be adjusted to any point along the transverse plane Once set it will crop out the image below the plane it has been set to Shown below is reorientation with right and without left gut cropping The gut contains a region of high activity thus the ellipse is erroneously matched to this area L The Gut Crop slider can be used to crop the gut to fit the ellipse to the LV more correctly R FlowQuant User Manual 63 Additional Documentation Rest Stress Defect Analysis Output File Guide guide to the text file output for Rest Stress analysis http www lightbox ca mfi FlowQuant Documentation Rest Stress 20Defect 20Analysis 200utput 20File 20Guide pdf Mismatch Scores Output File Guide guide to the text file output for Mismatch analysis http www lightbox ca mfi FlowQuant Documentation Mismatch 20Scores 200utput 20File 20Guide pdf Volume Viewer User Manual instructions on using the Volume Viewer tool http www lightbox ca mfi FlowQuant Documentation volViewer 20Manual pdf DICOM Convert Server User Manual instructions on installing and configuring the DICOM Convert Server http www lightbox ca mfi FlowQuant Documentation DICOM 20Convert 20Server 20User 2 OManual pdf
50. tudy Load Study F Save Study Add Analysis Entry Add Scan Entry ik Remove Entry Duplicate Entry e 1 Settings FlowQuant User Manual 11 Study List A list of analysis entries that may be batch processed in sequential order This list forms the heart of FlowQuant and may be considered as a list of analyses that the user requests The entries and their fields have context menus that may be accessed using the right mouse button These context menus provide additional functionality that is specific to the entry The context menus vary with the entry and field that is selected therefore refer to the information below for more specific options Comments This field allows the user to type texts associated to the study which will be saved with the study and reappear each time that it is opened Buttons Several buttons exist on the GUI including e Study selection radio buttons selects which type of scan data location to add pr hci Add Analysis Della A4 Scan Entr DICOM Node Q R Local Files select individual image files stored locally Local Directory select an image directory stored locally e g DICOM directory DICOM Node Q R perform a DICOM Query and Retrieve from a preconfigured DICOM node e Add Analysis adds a new analysis entry to the study list e Add Scan Entry adds a new scan entry to the current analysis entry e Uparrow m
51. ure synonyms that will be translated into standard terms used throughout FlowQuant The list of terms is displayed in the left half of the dictionary and the synonyms of that terms are listed on the right When looking to resolve a state any synonym that is encountered is translated into the corresponding term same process for tracers In the examples below the terms Water OWater and H20 will be translated into Water The patterns SStress Adeno ATP of Stress will be translated into Stress Patterns are sought in applicable image file header fields and are delimited by characters spaces and by numbers Dictionary Editor A a Dictionary Editor Terms Synonyms Terms Synonyms Rubidium OV Vater Rest A SStress Ammonia E H20 Adeno FDG CPT ATP Fluoride UnknownStudy Rolipram Acetate HED Tc Perfusion CT Contrast CT v v vw v The dictionary defines synonyms that are replaced The dictionary defines synonyms that are replaced by their equivalent terms For example by their equivalent terms For example Rb is a synonym of the term Rubidium SRest is a synonym of the term Rest Data Export Dynamic Data Dynamic data can be exported to an Excel spreadsheet for further analysis Each entry that has been processed reoriented and sampled is included in its own sheet The sheet contains a table about each time frame rows Data Export KM Results This tool is useful for
52. uto estimate RC automatically determine the recovery coefficient to be used for partial volume correction Recovery Coefficient preset recovery coefficient if a constant RC model is used 0 1 DV K1 K2 preset distribution volume value if a constant DV model is used Retention integral means by which to obtain the retention integral for the retention model Use default Peak constant time 0 2 min Time Gamma fit Blood input regions of the blood pool used to generate blood time activity curve for kinetic modeling and retention model Options include All combinations of atrium A base B and cavity C ROI generated from an early blood pool image External file RV blood correction optional correction for RV blood spillover into the myocardium ROI Fast flag choose either to process each sector of the polar map or of sectors and interpolate used to speed up kinetic modeling processing Default Yes No Coronary Artery Tree FlowQuant User Manual 45 Locations of stenoses can be entered for the major arteries The arteries will then be displayed on the polar maps and 3D views of the LV Anatomy options include default none right dominant left dominant e Extra TAC File Select an external file containing a TAC to which TAC from the scan can be compared Supported formats are comma separated variables csv files from GE micro volumetric blood sampler and Siemens IRW and Asipro so
53. verage activity over depth of myocardium Radial sample epi mm the distance from the center of the myocardium to the epicardium Dynamic smoothing Type type of smoothing Default Gaussian Uniform Peak to apply to dynamic volume sequence prior to obtaining dynamic polar map Kernel size size of the kernel used in smoothing Uptake the frames which are summed to generate an uptake image The default is 1 meaning the last frame However the user can enter integer numbers to indicate the last N frames to sum The user can also specify a range of frames from anywhere in the sequence over which to sum Weighted Sum Default On Off Uptake resolution mm target smoothing resolution 0 20 mm of uptake images FlowQuant User Manual 44 O Normal uptake threshold the threshold in percent of maximum activity in the polar map above which sectors are regarded as normal Segment model the segment model 3 5 9 17 or 20 to apply to the polar map for analysis NRings the number of polar map rings to use with the segment model Kinetic Modeling Options O Start time mins number of minutes from the start of acquisition at which to start the dynamic data for kinetic modeling End time mins number of minutes from start of acquisition at which to end the dynamic data for kinetic modeling Blood spillover correction correct for blood to myocardium spillover A
54. wn in red The user may change the location angle and size by moving the lines points and ellipse respectively In the event that the orientation is determined based on that of another scan the size and or angle may be locked see Adding a Scan Entry on page 15 If however the user insists on changing the size and angle the lock at the bottom center of the window may be clicked Clicking the lock swaps between locked red and unlocked green states The Reorientation Tool contains additional information such as the orientation source in the transaxial plane figure and whether the position angle and size of the ellipse in each slice was automatically determined manually determined or fixed The signal to noise ratio SNR and myocardium to blood ratio MBR are displayed in the mid VLA and mid HLA frames and file information is displayed in the basal SA frame The intention of this tool is to minimize user bias Therefore intervention should be at the early stages such as selecting the plane and gut The user should look for good overlap of the synthetic ellipse diagrams with the LV in the image In addition the last bottom right image is of a short axis slice through the base of the LV and should have a centered circular pattern The tool does not need to result in a perfect fit since final registration and sampling of the LV occurs in the next step LV Modeling Sampling The LV modeling stage detects the exact location of t
55. wse JetBlack Y E A Format E 8 Portable Network Graphic png v Preferred Uptake Units Activity Bq cc Mi DICOM Push Node Name None M OK Cancel l Revert to Factory Settings r Default Analysis Options SPECIES TRACER Defeut_Ls Polar Map Options Radial search 100 200 140 Radial sample endo mm 2 Radial sample epi mm 2 Dynamic PM Type S A smoothing Coussin Kernel size 15 Uptake frames Weighted off v E Uptake resolution mm 0 20 12 Normal uptake threshold 36 80 Segment model 47 wl NRings 16 Y Remove Kinetic Modeling Options KINETIC MODEL v Start time mins End time mins Automatic motion correction lott v Blood spillover correction lon F Auto estimate RC on ml Recovery coefficient 0 1 i DY OK L Retention integral se defaul O Peak time 0 2 O Time Blood input O Gamma fit ABC RY blood correction RY only v Fast flag Yes G Rest Stress Flow Analysis Options Normal Rate Pressure Product RPP 8500 mm Hg bpm Normalize only if RPP is greater Defect Clinical Classification Method coua x Apply Rest RPP ves M Confidence Intervals zz S a O absolute Stress Flow 20 O ML iminig Color Scheme Generate Summary Report Flow he General Options The general options pertain to the general functioning of FlowQuant and include the following options
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