Fratoria DICOM RT Studio
Contents
1. image while pressing the ALT button on the keyboard has the same effect it closes the contour 5 12 Magic Draw Extrapolate With the Magic Draw Extrapolate tool the active contour can be propagated to a next or a previous slice The grey values of the destination slice are taken into account so this is not just a copy contour tool 5 13 Add Contour Whenever a new contour is created it must be added to a Region Of Interest ROI This means that before one of the tools that create a new contour is selected the Add Contour tool must be chosen In the Add Contour dialog a name can be typed for a new ROI or an existing ROI can be chosen from the dropdown list If however you select a tool from the toolbar and no contour is currently active the Add Contour dialog will display automatically Add to ROI esophagus Figure 44 Add Contour window 5 14 Delete Contour 13 If a contour is no longer valid for use it can be deleted with the Delete Contour tool After confirmation the active contour is deleted from the ROI 5 15 ROI Manager With the ROI Manager tool existing ROIs can be edited or removed from the data set All ROIs are listed in the ROI Manager s main window Ml etrophanmasaa Figure 55 ROI Manager If a ROI is selected in the list the Remove button will remove the ROI from the data set The Edit button takes you to another window in which the ROI name and t2. lt Fratoria BV O Westewagenstraat 60 3011AT Rotterdam 2 e The Netherlands Fratorla Email info fratoria com imaging the future Web www fratoria com Fratoria DICOM RT Studio User Manual for Contouring Release 2 0 0 October 2011 C 1639 man Bb WwW N Contents Installation ASTUCIA tio aa 4 MINIMUM Hardware Requirements e rio ees 4 DAVIS Dat EEE 4 TOO atan ia oi 5 O RR 5 5 1 GONG A e tetas ONO 6 5 2 A O 6 5 3 Mera Pi e CS O E O E O santana racdacetanese seeoncesswenanaenceeait 7 5 4 Expand RO ean anna RCo a i PUR eR IR 7 5 4 1 Simple EXpansiony Contract visi a dictaba 8 5 4 2 Advanced Expansion COntractiON ccccccccccnnnnnnnnnnnnnononanananaconononononananonononon ono nnnnnnnanannns 8 5 5 A obaciaiee nasa erste pas uae scoop alsa ce stn ome tied Oa alee penance tunea ebwapdageece sean tauoas 8 5 6 SCISSORS oss es eset ase ction ceee catia ae rece tie ca oe depuis aaa tice yea cuueeenenoruemeaeroueaenss 9 5 7 BTS c ENEE aco EEE A T TE EA E E A ate te tase nome ce EATE TAT 9 5 8 O a a A 9 5 9 NA LS aos ins pause eaten E seg cvs eae ciac acest eeascienec eco aa goa anced ae antietinde suaeaaes ene 9 IIO sAULO SCEINEMCALION Vina Osso 9 DO AUtO sesmentation Step Lia 9 10 2 AUTO SESIMENTATION Step oe 11 35 10 39 AUtO SEEMENTIION MOD iaa 12 Sl MAI D AWe a a N tod 12 SA42 Masia DrawiExtra pole iaa 13 S3 Ada CNA ll dad Dado 13 Sd Delete Contour i 13 So ARONMaN tentado 14 Device description Fratori
3. 6 Expand ROI dialog 5 4 1 Simple Expansion Contraction With the simple expansion a margin can be added expansion or subtracted contraction to resp from a single ROI The margin that is input is always positive the selection Expand Contract indicates whether the margin is added or subtracted from the ROI Of course the destination ROI name has to be given so the application knows where to put the result 5 4 2 Advanced Expansion Contraction With the advanced expansion different margins can be applied for the lateral anterior posterior and cranial caudal directions Also Multiple ROIs can be selected for expansion contraction and multiple limiting ROIS can be selected to influence the new ROI creation The name of the destination ROI must be input 5 5 Scale With the Scale tool a contour can be moved around or resized When the toolbar button is activated a light blue box is drawn around the active contour Moving is done by pressing and holding the left mouse button while the mouse pointer is somewhere inside the box and then move the mouse Resizing is done by sliding press and hold left mouse button one of the sides of the box This way the contour is resized only in that direction To resize the contour in both horizontal and vertical direction simultaneously slide one of the corners of the box 5 6 Scissors With the Scissors tool a contour can be split up into two or more contours Press and ho
4. 7 at least 1GB of RAM and 1024 x 768 screen resolution The 64 bit version requires a 64 bit Windows platform 3 Saving Data The contours can be exported to a PACS or to a local directory If the destination for the export is a PACS a local copy can be saved by selecting the checkbox The directory of choice for the copy can then be selected or created For the export to a PACS the storescu utility from the DICOM toolkit is used If a local export is selected the user is warned if the destination directory already contains data for the study that is exported He can then decide to select or create a different destination directory or to overwrite the existing data Save in PACS Select PACS Host localhost AET CONQUESTSAVI Port 5678 Create a local copy of the exported data in directory Dtemp 1 Save on disc Store in directory E Wtemp copy Figure 1 Export Dataset 4 Toolbar 2 h Ww eee ae ee oe 16 rot to t tl oele 4 GROORFSLV RARRAF Figure 2 Toolbar Paint draw and adjust contours using a circle with a variable radius Magic Wand create a contour in 2D automatically based on gray values Expand ROI expand and contract ROIs by providing a margin Scale scale or move existing contour Scissors cut contour in two or more separate contours by drawing a line Eraser delete points in contour Edit show points in contour a
5. a DICOM RT Studio is a software toolbox for advanced radiotherapy viewing analysis and contouring based on DICOM and DICOM RT It allows the user to read all relevant radiotherapy data including images plans dose ROIs POls and RT images view this data interactively in 2D 3D 4D and evaluate plans This manual covers the contouring module that is available as a plug in and allows the users to do contouring and save the result as DICOM RT structure for use by other systems in the delivery of treatment to a patient Fratoria DICOM RT Studio runs as a stand alone application on Microsoft Windows platform The contouring module requires Fratoria DICOM RT Studio to be installed on your workstation Intended use The contouring module is for the purposes of creating patient treatment plans in radiotherapy Treatment Planning Systems with the contouring data generated and exported by this module Intended audience This manual is written for radiation oncology professionals and for Fratoria software service engineers You should make sure that you have thoroughly read and completely understand the manuals and release notes that are delivered with the software If you suspect that the system does not operate according to this manual discontinue its use and contact Fratoria customer support by email via info fratoria com CE Marking Fratoria DICOM RT Studio is CE market to the Medical Device Directive 93 42 EEC C 1639 Disclaimer All rig
6. es in the right hand side of the window the right hand Update button is clicked The right hand image shows the volume that is detected in 3D This can be rotated and zoomed the same way as the volume in the main 3D view The volume is sliced in transversal direction which creates a contour s for all transversal slices involved After pressing the Accept button the generated contours are placed in the transversal slices as RT Structure Sets 5 11 Magic Draw The Magic Draw tool is a drawing tool that sort of helps you in defining a contour Without the magic part a line is drawn between the exact positions of the mouse clicks in a view This can be desirable but often the contour is drawn along the boundaries of a part of the image that visually deviates from its surroundings grey value wise that is This deviation is detected by the Magic Draw 12 tool and thus the line points are added near or at the mouse position somewhere in the blue box in such a way that the tool thinks is the correct position driven by the grey value of the previous point that was added Figure 33 Using Magic Draw With the Magic Draw tool a line is created either by clicking the mouse at different positions or by dragging click and hold it If a point of a line is in the vicinity of the mouse position the next point added can be at exactly that point thereby closing the contour and making it valid Clicking in the
7. he contour color for that ROI can be set Name ERR es OK Figure 66 ROI Info 14
8. hts reserved 2011 Fratoria BV All the information in this document is intellectual property of Fratoria BV The content of this document may not be reproduced or published without written permission from Fratoria BV 1 Installation Instructions Contouring module is a plug in for Fratoria DICOM RT Studio Two versions of the plug in are available 32 bit and 64 bit depending on whether you have 32 or 64 bit version of Fratoria DICOM RT Studio Prior to installation of the Contouring module install DICOM RT Studio with a floating or static license see installation instruction in the DICOM RT Studio User Manual The Contouring module does not require license information during installation process A user can input the license information when starting DICOM RT Studio with the installed Contouring module for the first time or pass the license information to the installer using arguments when the installer is run from the command line or in an Active Directory environment Contouring module installer flags for installation from the command line NetworkContouringLicense StandaloneContouringLicense LicenseServerAddress LicenseServerPort Example Fratoria Contouring Module msi NetworkContouringLicense abc123ContouringLicenselInfo123 LicenseServerAddress 192 168 0 1 LicenseServerPort 556 2 Minimum Hardware Requirements The 32 bit version will run on any Windows based PC laptop with Windows XP Windows Vista or Windows
9. ld the mouse button and then move across two or more line segments Each line that is crossed is cut and endpoints are added to it If two or more lines are crossed one or more lines are added between the cross points in an effort to keep the thus created contours valid At least two line segments must be crossed for the scissors to work 5 7 Eraser With the Eraser tool points can be deleted from a contour The adjacent points of the erased point are connected With the spin control in the toolbar the size of the eraser can be adjusted in a range from 5 to 100 Size 9 Figure 7 Eraser size input 5 8 Edit Use the Edit tool to edit a contour point wise Each endpoint of a line segment is highlighted by a small square around it Points can be dragged to move them Also the Edit tool can come in handy for use of the Eraser or Connect tools 5 9 Validate Contours can be validated by the Validate tool A valid contour is closed contains exactly one enclosed area and has no self intersections If e g the validated contour is not closed the following message is displayed Contour is not 1 closed area Figure 8 Contour validation warning Other messages exist to point out issues of the active contour If a contour is successfully validated a message saying Valid is displayed 5 10 Auto segmentation The Auto segmentation tool can be used to create ROIs semi automatically By defi
10. ning a few rules contours are created in three steps based on grey values over multiple slices 5 10 1 Auto segmentation Step1 Define a cropping filter in 3D This cropping filter is defined by indicating a bounding box in each of the transversal coronal and sagittal views Actually both the coronal and sagittal views define the same boundaries Z direction so if the boundary is changed in the coronal view the sagittal view will be updated accordingly The transversal view defines the surface on which the segmentation is performed per slice This is indicated by the red rectangular shape like this Transversal Slice 47 of 80 X Y Z Scalar Value Dose Value Figure 9 Auto segmentation step 1 transversal cropping filter The red rectangle defining the surface can be resized by dragging click and hold one of the little squares on the inside of its boundaries As said both the coronal and the sagittal view define the distance in Z direction the number of slices over which the segmentation is to be done As they define the same variable only one of them is needed Below is an example of this sagittal view 10 Sagittal Slice 258 of 512 X Y Scalar Value Dose Value Figure 10 Auto segmentation step 1 sagittal cropping filter The distance in Z direction number of slices is defined by the distance between the two red lines This distance can be changed by dragging click and hold the red
11. nts that fall between entering the circle and leaving it are deleted only if the result is still a valid contour This way the contour can be kept clean from cluttered up points Transversal Slice 1 of 80 Selected Contour jghkf Bm Scalar Value Dose Value Figure 4 Result of pain tool on CT image 5 3 Magic Wand The Magic Wand tool creates a contour automatically based on the gray scale values in the image at the position that was clicked with the mouse It scans the environment around the clicked position and expands the area until a significant difference in gray scale values is found Using the Magic Wand tool bony structures or tissue parts are easily marked The tolerance for the gradient that is used in the algorithm can be set with the spin control in the toolbar as indicated below Tolerance 23 Figure 5 Magic Wand gradient tolerance 5 4 Expand ROI Expand or contract a ROI with a specified margin Two types of expansion contraction currently exist e Simple expansion contraction e Advanced extraction contraction Simple expansion contraction Source ROI Expand contract ap Destination ROI name Contract Prostate expanded Advanced expansion contraction Available ROIs Source ROl s Urethra Rectum Margins in mm Expand contract Lateral Ant post Cran caud 5 5 a Expand S Contract Destination RO name Prostate expanded Figure
12. ontouring tools however affect the currently active contour only Note that this means that after a contour was painted with e g the Paint tool the Magic Wand is selected and the user clicks somewhere in the active view the active painted contour is lost All of the tools perform the action that was requested by mouse actions sometimes in combination with use of the keyboard except when the requested action will result in a contour or ROI that is not valid in that case no action will be performed 5 2 Paint With the Paint tool new contours can be drawn and existing contours edited The mouse pointer is shaped like a circle of which the diameter can be adjusted through the toolbar Radius 10 Figure 3 Paint tool radius The initial contour that appears when the left mouse button is pressed in a view is a red circle depending on the line color settings in the main toolbar that is positioned at the mouse pointer After a contour has been created it can be altered by pushing the line in the direction of choice press and hold left mouse button while moving Contour points that fall within the circle are drawn to the edge of the circle using a shortest distance algorithm Contour points that do not fall within the circle are left untouched Extra points are added when needed this way a contour can be customized as seen fit By pressing the ALT button on the keyboard and the left button on the mouse the poi
13. s squares You can move the points with the mouse Validate verify if contour is valid 9 10 11 Auto segmentation step 1 2 3 to create 3D contours semi automatically 9 Auto segmentation Step 1 Define bounding box in transversal coronal en sagittal views by means of cropping filter 10 Auto segmentation Step 2 specify the middle of the cropped volume by placing a seed 11 Auto segmentation Step 3 generate 3D surface preview and extract contours 12 Magic Draw draw free form line that follows the edges based on gray values inside the square that follows the mouse cursor 13 Magic Draw Extrapolation automatically copy and adjust edges of a contour on next previous slice 14 Add Contour add new contour by entering its name 15 Delete Contour delete individual contour in a ROI 16 ROI Manager edit change name and color and delete ROIs o N DWM BWN FE 5 Tools 5 1 General During contour editing the currently active contour is always indicated by an orange arrow pointing down from the highest point of that contour When a different contour should be edited use the Select Contour button in the main toolbar In order to create a new contour button 14 Add Contour must be pressed and a ROI must be chosen or created for the contour see par Add Contour Contours that belong to the same ROI a ROI can be and often is spread over multiple slices are all affected by ROI operations Most c
14. triangles up or down If the sagittal view is altered the coronal view is updated accordingly and vice versa The 3D view displays the 3D volume that is defined by the above described step 1 of the Auto segmentation tool 5 10 2 Auto segmentation Step2 Step 2 is needed to define the center of the cropped volume defined in step 1 This is done by manually placing a seed in the transversal view The seed is indicated by a bluish dot which is actually a sphere Figure 11 Auto segmentation step 2 seed 11 5 10 3 Auto segmentation Step3 Auto Contouring Image input Result Level Lower threshold Window T9 Upper threshold Conductance terations Figure 22 Auto segmentation step 3 3D propagation Step 3 propagates the sphere from step 2 in all directions growing a volume based on the grey values encountered Several settings influence the 3D propagation these are set in the window for step 3 see above They include the level and window settings a k a brightness and contrast the conductance which is a kind of smoothness of a filter that is used on the image and the number of iterations the algorithm performs which influences the accuracy The more iterations performed the greater the accuracy but this can result in a performance penalty After accepting the values set in the left hand side of this window the left hand Update button is clicked and then after accepting the valu
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