Carimas 2.4 User's Guide
Contents
1. Project Settings Local Settings Show Dynamic Images With One Frame as Static Dicom PACS search fields It opens the Dicom Hosts panel Machi i d Local 4E Title FO aan name I Use Host List zerverAE Display ame Mewh ost Address 127 0 0 1 Fort 104 ListeningPort 104 Add New Remove Selected Ok The panel lists all DICOM hosts that exist for the current user Select the DICOM host in the Host List left and see properties of this host Here you can also define the Application Entity AE title of the local client Carimas machine If this field is empty machine s name is used as the AE title Images are retrieved with C MOVE which means that Carimas is a server that the DICOM host is communicating with therefore needed is the listening port field IP AE and port of Carimas client must somehow be defined in a server side for data transfer Queries will work without 6 1 2 Configuring PACS search field list User can make search queries by any DICOM tag To define the search fields click the PACS search fields button on the Local Settings tab page Local Settings Show Dynamic Images With One Frame as Static Dicom Hosts PACS search fields It opens the Configure Search Attributes panel Configure Search Attributes x 0010 0010 Patient s Name 0010 0020 Patient ID OE TU Study Description 0010 0030 Birth Date 0010 0040 Sex Name Patient s Name TagString 0010 00102. Cube segmented regions are Bami Bani listed in the TAC f yoxs BB 1sted 1N the S pane Volume mm 3 Times min 0 04167 2717 8 3628 9 0 125 41 794 47 545 0 20833 179489 220419 3 The Table and the Plot A 315256 374515 4 296 846 359891 4 281103 344352 5 250863 308133 218256 262247 186635 223679 171878 202944 143103 171425 Values and times of the selected curves are displayed in the Table window and plotted as well 4 2 1 Calculating max curve By default Carimas calculates TACs by calculating a mean value for each frame It is also possible to calculate a so called max curve by finding a maximum voxel value for each frame To calculate the max curve check the box of the needed region s TAC it should not be loaded from a disk Select All Select All Subltems Unselect All Model lt Mone gt Properties of highlighted TAC The max curve will be calculated and added to the TACs list 4 2 2 Changing output time unit Output time can be switched between minutes and seconds from top right region of the plot window Changing output time unit Values Of Selected I a Times of both plot and table are T i boui WINE SFCOong A updated Th
3. 11 SRE 11 SEH ll lO ll SEE 114 SEED Jl Jee 3 2 3 Using VOI filters You can use several VOI Filters from the Tools Menu 3 3 Tools for all ROIs VOIs The File and Edit buttons help you save load and modify the ROIs VOIs you created Fies Est New 3 3 1 The File button options Clicking the File button you can choose to load already existing VOIs or save the created ones Carimas offers you options to save all the VOIs Save All VOIs or only selected ones Save Selected VOIs Load VOIs From File Save Selected VOIs Save All VOIs C None C Vertex Whole When saving the VOIs you have options of the saving format File name FO Save as type VRML files vrml 3 3 2 The Edit button options The Edit button offers you to perform all general functions on your ROI VOI such as Cut Copy Paste Delete and Rename Cut ctrl x Copy ctrl c Paste ctrl v L Tall Delete delete Mirror selected V Is Rename F2 Combine Selecting Mirror selected VOIs lets you create new VOIs associated with the existing ones without much effort Cut ctrl x Copy ctrl c Paste ctrl v Delete delete X Axis mage center Rename F2 Y Axis image center Combine Z Axis image center X Axis current cutpoint Y Axis current cutpoint Z Axis current cutpoint B
4. 5 2 Saving results of AIAN SIS R R a ai a i a i det racic E a 30 S 0 6 010 U0 S aaa ESSR NSS iii i a o i A 30 6 FACTIVA S UE UO ii iii i iii i ii i ii i i i i i i r i 32 GL Localcomputer Sene sea kasai is ba ka i a i i a i a i i i as 32 6 1 1 Common PACS Server S i iii ii ii iii i i i iaaa 32 6 1 2 Configuring PACS search feld iStrane i iai ij i 33 Cka VLG UNS CEE S aaa reiia ai ai i e i eee es 34 Ol CS EOM CO LOL Iie ais ai a i a i i a i i a a a a a eee 35 6 2 Application log and error 109 imis ini iii iii i ij ai i i i i i 35 Oi ProjectGat VSV asset eba bau 36 GROSS AV iii iii i a la V a o i i i i kua ao i ls 38 1 Loading images to Carimas Once you have opened Carimas you are presented with the Load panel which invites you to load images either from your local drives Open Local or from picture archiving and communication system PACS available at your institution Open PACS Open Local Open PACS 1 1 Loading from PACS Carimas has a separate dialog box for PACS communication You can open it by clicking the Open PACS button DICOM host from where Search fields Runs the query Search fields the search is performed Load Images From PACS Search Time Ae S kd a G PetPACS Research The time range of Mo Limit C Range the search query C Past 24 Hours From 20102011 I Patient s Mame test Fast Days To 2010 2011 vf Patient ID Study Description Search results of
5. Description Patient s Hame Enabled True 000s 0050 Accession Number 0005 0050 Referring Physician s Marne 000s 0061 Modality 0008 103e Seres Description Add New Remove Selected Ok All DICOM search fields are listed on the left Select an item on the left to see its properties on the right The four listed properties are a TagString The DICOM tag that is used for search query in following hex format XXXX XXXX b Description Description text that is shown to user in tool tip when user moves mouse on that search field c Enabled With this flag it is easy to enable and disable search fields if some server does not allow this DICOM tag or administrator wants to keep the search panel look simple and disable some fields without deleting the whole search tag enabling is later easy d Name Short caption for filed that is shown in search panel like Patient s Name You can add new search field by clicking the Add New button Remove Selected it creates a new Search tag with empty property fields Fill all the properties and the search field is ready to use 6 1 3 Window flip settings These settings are exceptional and should be used with caution by an experienced user The settings let you change the image orientation They are useful if your image s orientation is wrong and you want to change it without flipping from the Image menu 34 Window Flips Transazial s Y CZ Sagittal CO 4 T
6. Execution directory Iz Li O TekslectiCarimazMainTrunk CarimazBazicibiniKeleazE Application Data directory is C Documents and u Settings pirat Application Data arinas SA onu starting to tind plugins fram folder 4 O Tekeleet arimazMain TrunksCarimasBasicchinJrelease Pluc 7 Vern a n Different log levels are shown in different colours Debug is gray info is white Warning is yellow error is light red and fatal error is red Detail information about currently selected log item The errors and fatal errors contain often lots of exception and trace Source Data ree information about error that is Thread MainPanelT hread listed here Je Change Toollode General Old F ar kl IA 6 3 Project data viewing Current Project Data q In x Volumelnterpolation Nearest eighbour FillMethod Two ayBresenkam All data currently stored in the project can be seen from selecting View Project data from menu Project data dialog will open The data is categorized in tree structure that can be browsed with panel on top region of the dialog The text box on low region of dialog lists the contents of selected node in xml format This xml is written same way as it will be in the project file xml when the project is saved Here user can see and get information that he she cannot get with normal Carimas GUI like see or copy point coordinates of some ROI to clipboard etc 37 Glossary 3D volume rend
7. a time unit If the unit is ms time is displayed as L minute or second in all plots and panels depends on current output time setting Modification Cancel Apply Ok 4 2 4 Loading and saving curves Carimas supports loading of external TACs in DFT from a disk TACs can be loaded clicking the Load button from the TACs panel Saving is handled from output display windows Value Vers elected TACs Save To TXT Save Ta DFT Voxels eson Selected curves can be saved 166254 J MM into disk with save to TXT from disk and adds them Van and save to DFT buttons into the curve list Values seen on table are saved 4 2 5 Modelling Running a model against a set of TACs The first step of a modelling process is to select a model and prepare it for the fitting process The four sub processes are described in the picture 24 4 Define limits and initial guess values 1 Select correct 3 If you want to define model with parameter limits open model selector model options with options button for parameters of model Modelling TEE Model Heart oxyqen 15 Parameter Hin Max Initial Guess water model Fiml a4min A E 0 5 ___ Input Functions Walral rl A 05 i E m function Not Set a cs 2 If the model needs functions this list is shown Set inputs by clicking the correct input function name from the list only one in the example Program will ask you to choose
8. the correct input among curves of the project The second step is to select the TACs to fit and define the modelling time range The model is fitted separately against all these curves and the best fit curve and its parameters is chosen for each TAC The five sub processes are in he the picture EE a k El V Ry Tube i s n Cube 1 Select check the curves from list to fit allows youto EP Bai 5 mum initial guess 280 Model Options odel 200 nd Parameter Min the model 4 Select Fiml g rnin ic correct time Va ml mi 0 05 PT Fm 0 05 range using min 2 If you want to fit only Specific time range click model options 3 Check the Define time range box from the dialog that opens Actions S Model Heart oxygen 15 I Define Time Range 4 Min and max modify bars will become active in plot window Third step is to run the model It is done simply clicking the Fit to TACs button from model panel Modeling Model Heart oxygen 15 water model gt Options Input Functions i function Whatever Fit to TAGs 4 2 6 Inspecting the modelling results After model is fitted to all selected TACs the plot will show the fitted curve along with the original curve Original curve is visualized as dots and fitted curve is a solid line Modelling results panel will display best parameter v
9. unit of volume corresponding to the smallest element depicted in a three dimensional image the signal from which contributes to the intensity of the image
10. CZ Corona 4 E 6 1 4 Custom Colours You can customize the colour settings of your Carimas Colors ForeLolor BackgroundColor Gradient Gradient Panel Light 6 2 Application log and error log Application Log can be opened from View Log All messages of the program are displayed with this component Log dialog is run separate from other Carimas GUI so that Carimas can be used when log is displayed Log messages of Carimas are categorized in following five categories a Debug Lowest level and it lists the most detail messages that can be used for tracking errors b Info Message that gives good to know information to user c Warn Message if something exceptional was done that user needs to know about For example if some part of data could not be saved with selected format and were ignored d Error Message that is shown if some command of user was aborted for some reason e Fatal Message when there has been error in program itself All this kind of errors should be reported as bugs All errors of this level are automatically written into special error log file that is found from user s personal application data folder 35 Level of displayed log items Also all items of level above selected one are displayed Application Log M Log items List of log messages Time log level and messages are displayed for every item ID x Log Level Debug Time Level Message A
11. Carimas 2 4 Core User s Guide Contents 1 Loading images to Carimas ssssssusussusunnunnnnunnununnunnnnunnnnunnnnunnnnnnnnnnnnnnnnnnnnnnnn nananman annan nnnnn nananman annann na 2 Mees Loading irom PAGS PEN tea i i a a a a i a aa 2 T2 Feo ate MO GE AL Ik asa ures i i i i i errr te i a tere ert 3 1 3 Loading from a command line kiaaaaaaaaaaakaaaaeasasaseasaaaasa saaa a aaa aaa aaa aaa aaa aaa 4 14 Viewing Mie image Ncadde Fanio siai asi aa ii i i i i i a i i 5 1 5 Preparing loaded images for visualization s erx4eoxex4eexrrteexereteexeeeteeneeeoeeeteten ten 5 1 5 1 Main and Background IMA S Lininis sa a isiikininiskssss sink uk ia siai inkai a si ia i i si 5 1 5 2 Lie E EA MAC E MPS ARO i ii ia ai ea EN 6 1 5 3 PD PMS image AL asi iais ia a ai a ia i a i i is 6 2 VISUAL ZA OK iii iii ii iii ii i ij ii i i i i i i i ma i i i i e 7 2 1 Interacting with graphical WINdOWS s s eeeseeeerereoeererereonoeenre te sa a aaa aaa aaa aaa 7 Focal DON ea hs CN k so keisis a i a A aiSia 7 2 3 Visualizing smaller part of image With 3D windOW ss ss sssssssssssressrrsnsnensnensreesrnsnnnrnnnrnsnnennnnnnnrennnes 8 LA Sea S 8 2 5 Custom 2D slice directions instead of tansaxial coronal and Sagittal 0 9 3 Segmentation of loaded images Lissist is i niississusiuskiasiss iai usduski an sau akn sas sa ij sa is ia a 10 PA ROS o a paisa ai iii i ii i a i a ii ner 11 3 1 1 Selecting type 0 ROL i
12. F aky GEOS7 015 001 Test 12012011 the guery have a F ake GEDG7 015 001 Test2 12012011 The Load button that tree structure db ROtest 03022011 ROttest 03022011 becomes active when a E studyDate 20110203 AccessionNumber Desc series or an individual FE PT Date Description TPC_AIVO_35cm_4 slice is selected from the search results panel Patient gt Study gt Series gt ImageSOP oP Load Into LCarimas The search follows five steps 1 Select target DICOM host search fields time range 2 Click Search 1 2 3 Select correct series or individual slice from search results panel Click the Load into Carimas button that becomes active when series or slice is selected 5 The image has been loaded into Carimas Load more images the same way or click the Close button Loading from a local disk To open images on local drives click the Open Local button Open Local Open PACS The standard Open File dialog box will appear you can load images of all formats supported in TPClib x J J E gt Computer DATA D3 Carimas 2 4 v K Search Carimas 2 4 2 Organize New folder 0 Sir Favorites 2 Name Date modified Type Size EE Desktop JE Plugins 20 10 2011 19 16 File folder Downloads amp carimas 20 10 2011 14 45 Application 1198 KB ai Recent Pinces E ColorScales 18 10 2011 10 15 Configuration settings 2KB BB Libraries DataTree dll 20 10 2011 14 44 App
13. If image opens in wrong orientation image data can be flipped from Image menu Flips are flipping the currently selected image see selected image chapter It is good to check the flips before drawing any ROPs because flips affect only to selected image not to ROIs File Edt wiew image Tools Help CEEI D aim Re ig Flip Front Back Flip Head Feet 2 Visualization 2 1 Interacting with graphical windows When you have an image loaded it is centred to all windows so that it is fully visible Dap Sagittal Slice 65 128 Baimi The camera of 3D window is placed so that it shows the whole image thus the general look of the image can be easily seen by rotating the 3D camera around Normally the start and end colour bar values need to be adjusted for getting good 3D visualization 2 2 Focal point and screens There is always one 3D focal point which is the basis for all visualization windows When image is loaded this focal point is automatically set to a centre of the loaded image All 2D windows have grey horizontal and vertical lines which cross at the focal point 3D window is centred to this point so that the rotations will be around it and zoom will be towards it Slice positions of 2D windows are also calculated from this point Focal point can be moved in the Cut mode shortcut is the Alt key a mouse click or dragging the mouse in 2D windows In the 3D window double clicking on a voxel will set focal p
14. New Times Close Menu Open Local Open PACS You can save the started project either from the File menu Edt View Image Tool Help New Project Open Project Open Image Open ROI or from the button row File Edit View Imag You can save any picture in Carimas a projection view a 3D view a TAC etc at any step of working with the image Right click on the image select Write To File as Bitmap Write To File as Bitmap Print Print Page Setup Print Preview And select from a few publication friendly image formats L IPG files jpa TIFF files tiff PNG files png t b TILT To save the created ROIs VOIs at segmentation step select the VOIs right click in the VOIs panel and select Save Selected VOIs Cut ct Copy ctrl c Paste ctrl v Delete delete Rename F2 Unselect All Combine File name Name them Save as type vRML files vrml VRML files vrml Imadeus ROI files roi Mask Image 8 bit analyze Mask Image 1 bit analyze Saving results of analysis To save results of a static image analysis click on the Save To TXT button near the table with results Save A TAXI To save the results of a dynamic static analysis click on Save To TXT button to just save modelling results click on Save To RES to save the modelling results with more information on the modelling method date of the analysis etc Although the Resul
15. alues of fitting process for each of the selected TACs Only the points inside the time range are fitted ae 40 000 x Fixed Heat ear 0 LS 2 28 3 6 m Segment Analyze nalyze Report o 16 24 3 2 4 THEN Mg Only selected curves are shown on plot and tables File Edit View Image Tools Help EETPITEXI am In the Carimas Core Tab you can do all basic 32 operations Load images Draw ROIs 2i O0 Calculate and Analyze results 240 000 min Values Of Selected TACs Save To TXT ee Modelling Results Of Selected TACs Save To TXT Save To Tube Cube Cube Bami aim 48 077 Voxels 0 72708 Volume mm 3 144372 166254 0 49557 FitMethad be Heart oxygen 15 water mo ube Heart oxygen 15 water mo ss gt F mligimin Va mlimi PTF miiml Method Actions gt Times min 0 04167 naw 2717 8 3628 9 A4 704 a CAC Original TAC is show Best model as dots Best fitted curve from model as solid line Original TAC values are shown in this table parameters are listed for each selected curve It is always possible to do a new fit with different parameters or ranges Old results will always be overwritten 4 2 7 Patlak amp Logan with modified time range In Patlak and Logan case the running model again with different time range
16. as aras Ai ie a ii i i etter tr ij tenner eter ere ire 11 3 1 2 PROTO CHF OTN ON Sac DR iai i i i i i ss 13 e DVO KO ie ai i iii ia iii ei a iii A 15 Je Addis 4 D SA o R aisiais iii i i i a ferent rete 15 3 2 2 NES eae E i a i i 15 3 SMS VOLNE o 17 23 Took 6 AROS VO LS iai iii iii i i ai a eer ee 17 3 3 1 The EMS Dutton opUOnS PR O O aa a 17 39 2 The EcLLE Button ODU OTS Kenis ania i oi i i A ij i a a ei js 18 4 Analysis Ol segmented Terons susausissiaaisssiinisi is aaa eaaa aAA ERa 19 Ack E o e Ea EE ANA Y SIS E ii as e o i i si i i a i S 19 Aa Dn e ogre oo E DY e i i E eee 21 4 2 1 Calculating Max CUTVE sirissisiriisiananiiininnnadinansdeinndaniainanandaoanavadiana aandaa anida iaaaddnaniada iaaiiai naan 22 4 2 2 Changping OULU CC UNC A A 23 4 2 3 Curve properties times unit colour display Style s sssessssesssssrsssressrsnrrssressnenrnenrnssnenns 23 4 24 Loading and saving CUIVES cesesssesesesseesseseseseesesesceteeseseasenesesesseneneaeseaseneseaeaeeseneasseaseneeaeaeateneasaees 24 4 2 5 Modelling Running a model against a set of TACs ssssssesssssssssessressrrssrnsnsnensnessrnsnrnensnensnees 24 4 2 6 Inspectine the modelling FESUL S st ss nisisis ssisiiiks a 26 4 2 7 Patlak amp Logan with modified time range cccsesesesseseeesseseeeeesseeesesseneseeneeseenseseeneeaseneaeaes 26 5 Savine and Reporte lai iii iii i iai i i i i i ji ij i i i 28 5 1 Saving in Carimas before analysis has been CONE essences 28
17. circle Used are 17 segment AHA and 20 segment ASNC models Myocardial segments are named and localized with reference to both the long axes of the ventricle and the 360 circumferential locations on the short axis views ROI Region of interest a contiguous set of pixels in the PET image defined by hand or automatically normally used to track radioactivity in the set over time 2D self contained file A type of file holding not only the original itself but the information about the original metadata e g hdr containing all the acquisition information static image reconstructed data of a static scan a single frame acquisition with scanning after the injection stress image an image obtained through a technique for examining the heart s coronary flow reserve by imaging the patient during exercise activity or pharmacologic maneuvers intended to reveal areas of marginal coronary flow reserve caused by partially obstructed regions of the coronaries subtraction method an approach intended to localize the changes in the studied organ In this approach two different organ e g brain states are compared namely a control state is subtracted from a task state in order to create a difference image This image tells us which areas in the organ are involved in the task state VOI Volume of interest a contiguous set of voxels in the PET image 3D voxel volumetric pixel the three dimensional equivalent of a pixel a
18. e ROI and modify its position and adjacent sides as well as ROPs area move the cursor close to it and drag Move cursor to an angle and drag it Selecting the outer side will modify the ROI in the direction of the side you can stretch or shrink the ROI Selecting and dragging one of the angles of the outer ROI box will enlarge or shrink the whole ROI depending on the direction of the move 3 2 3DVOIs 3 2 1 Adding a 3D shape Click the New button to create a VOI select the option you need ROI Set ctrH R Sphere ctr B Cube ctrHU Cylinder ctrl L Tube Hollow Sphere Hollow Half Sphere Plate As you are creating a 3D object you will see its projections in all three images projections the VOI itself is best visible in the 3D window here we created a Sphere ethod Color gt Ee Bea Mes Lier JB Cut None gt B MAD B ml mi 2 53e05 3 2 2 Editing In any of the projections you can modify VOI projections the same way as ROIs 15 You can also use Vertex the moulding tool for fine changes f None Vertex f Whole Move Vertex AL On the slider fix the size of the Vertex small size grows from left to right select the part you want to mould and drag in the needed direction Clicking on the Change Color button you can select and change the colour of the VOI al E None Vertex g B ors
19. ering the process of reconstructing imaging data from serial consecutive Slices in three dimensions for display purposes DFT Data Format in Turku time activity curve format used in Turku PET Centre DICOM Digital Imaging and COmmunications in Medicine a global Information Technology standard that is used in hospitals worldwide Its current structure developed by the National Electrical Manufacturers Association NEMA in 1993 is designed to ensure the interoperability of systems used to produce store display process send retrieve query or print medical images and derived structured documents as well as to manage related workflow difference image the result of the subtraction method telling which areas in the studied organ are involved in the task state dynamic image reconstructed data of a dynamic scan a scanning producing several frames of fixed continuity fixed frame duration e g 6 five minute frames from 30 to 60 min post injection or variable continuity variable frame duration ECAT Emission Computed Axial Tomograph a self contained image data format used by the CTI PET scanners frame division of the data matrix that indicates where the image is located in time image fusion a process leading to graphical display of multiparameter data sets representing complex phenomena e g fusing MRI data with PET data PACS Picture Archiving and Communication System electronic systems develo
20. ion the process of classifying the voxels of an image into a set of distinct classes Zaidi and El Naga 2010 Click the Segment tab to enable the segmentation of the loaded image s The Segment Tab Here will be listed all created ROIs VOIs Functional buttons to create edit lt and load existing ROIs VOIs ee Click the New button to create a ROI Set or a VOI select the option you need ROI Set ctrH R Sphere ctrl E Cube ctrl U Cylinder ctrl L Tube Hollow Sphere Hollow Half Sphere Plate Click the File button to load the existing set of ROIs or VOIs I Load VOIs From File Save Selected VOIs Save Al VOIs 1NB Medical image segmentation has been identified as the key problem of medical image analysis and remains a popular and challenging area of research lt gt The difficulty in PET image segmentation is compounded by the low spatial resolution and high noise characteristics of PET images Zaidi and El Naga 2010 Creating VOIs from primitives might be a fast way and the only one needed in case of more or less simply shaped volumes some tumors bone sequestra etc if the volume of your interest is a complicated one you might prefer drawing ROIs in every plane and then combine the ROI set into a VOI Carimas will give you a lot of freedom in this matter Click on any option from the New list and the Edit VOI panel appears 3 1 ROI lists Clicking on ROI Set will ope
21. is more tricky because they produce fitted curve with totally different unit and scale than the original curves After first modelling round the plot will display the patlak logan plot instead of the original TAC which will cause time range selector to be in a wrong scale The easiest way to run the model with different range is simply to undo the last fit and do the fit again Another way is to uncheck the Show fitted TAC on plot checkbox the Fitted tab of the Curve Properties dialog box Up Show Fitted TAC on Plot Name TPClib Model Patlak Input Functions 26 5 Saving and Reporting All result displaying windows of Carimas have separate buttons for saving data that is displayed on it Curves are saved from TAC table window Modelling results from Modelling result table window Statistics from Statistic table window Plot has button for saving all curves that are currently displayed on it Also every window can be saved as bitmap file or be printed by using mouse right click context menu 5 1 Saving in Carimas before analysis has been done You can start saving right after you have downloaded the image into Carimas To save the loaded image as DICOM right click on the image in the Images panel and select Save Selected Image as DICOM Maint Brain 12 FDC dynamic PET Main Brain 18 FDG dynamic PET To Invisible Remove From List Run Filter to Selected Display Unit Bq ml Show Image Header Rename Load
22. is is also the unit used 2 7 ___ oxels EN when curves are saved into disk M volume mm fis LO NJ T Times min NAL o 28 0 8 44 0 375 min 0 45833 S 0 M6467 296846 359891 4 2 3 Curve properties times unit colour display style Every TAC object has properties that can be modified from the Curve Properties dialog box The box can be opened double clicking the TAC or clicking the Actions button Yalues Of Selected TACs Save TACs selecteq Select All Select All 5ublterns Showing properties of the TAC Unselect All Double click the TAC or highlight it EST 0003000 E F ties of highlighted TAC and select the Properties of Te se gt highlighted TAC from the Actions Calculate Max TOT VE menu 2 The Curve Properties dialog box Visualization properties for plotting Modification controls for x axis time properties of the TAC Curve Properties Properties of a Fitted TAC can also be changed if there is fit run against this TAC Name Cute Vict 20 M Show Lines Show dots Color Modify Time Scale x axis Range 2500 00 265000 00 msec Multiply Factor ji ime shift msec BO ren 1000 1000 E Modify Value Scale y axe Range 3628 89 374515 12 Bari controls for y axis data Multiple Factor ji properties of 10010 1000 the TAC Units can be manually changed Carimas recognizes only comi ms as
23. lication extension 61KB D Documents M DISCLAIMER 20 10 2011 14 15 Rich Text Format 14KB a Music m je63to7 0 9 6 10 9 2007 15 12 Application 107 KB Pictures GraphicsLibrary dll 18 10 2011 16 24 Application extension 13KB E Videos LocalSettings 18 10 2011 15 41 XML Document 4KB ener _ M_002 v 26 6 2007 15 06 V File 36 109 KB U os c PACsClientLibrary dll 18 10 2011 16 52 Application extension 1423 KB s DATA D TPCCommon dll 20 10 2011 14 44 Application extension 6KB ca SDATAI E TPClib dll 20 10 2011 14 44 Application extension 895KB Sa SDATA2 F Ed Filename zla E Open Cancel L For DICOM there is also an alternative option the Secondary Library which can be selected from the format drop down list All files ECAT files 4 Analyze files 1mg MicroPET files img DICOM files With Primary Library DCOM files With Secondary Library Images loaded with the Secondary Library will consume fewer resources Local opening always opens entire image series not individual slices So in DICOM by selecting and clicking on one file only Carimas will automatically load the rest slices of the series consisting of many files like DICOM 1 3 Loading from a command line Images can be opened also from command line by giving full path to the image In DICOM case there are two options full path to one slice and Carimas will open the remaining slices as well or give only folder con
24. n this variant of Edit VOI panel Edit VOl Ps Change Color Next ROT Trace r aie E 3 1 1 Selecting type of ROI Click on Next ROI drop down list and select which ROI you want to draw Next ROI Trace r Trace is the default one with it you create polygonal ROIs Left click mouse to set angles drag it to draw a side To close the drawn ROI drag towards the starting point The drawn ROI shows you the voxels that will be included in the analysis Drawing Rectangle Circle and Ellipse is straightforward and can be done with one left click and dragging the resulting ROIs to the needed size Drawing Spline ROI every left click gives a new bend closing is the same as with the Trace With Freehand you draw by dragging the mouse releasing the left button will close the ROI no matter where in image you released the button 3 1 2 ROI modify controls To modify geometry of the created ROI select it in the Edit VOI panel L Change Color Next ROI Trace T The RO Tra Going through the following pictures note the position of the cursor its position relative to the ROI determines how you can modify the geometry of the ROI To move the ROI place the cursor in the centre see the red intersection appear drag in the needed direction To rotate the ROI around its imaginative centre move the cursor outside ROIs borders see the red circle appear drag as needed To move a side of th
25. oint on it Also the Move tool of 3D window moves the focal point v 243 3 9 J Rendering Methods i r PAS Method Color gt E Dracos Cut Quater gt Na Focal W Point PNN u Cut Modes are TW oe different ways to N cut blocking voxels v between camera and focal point here Quarter cut 2 3 Visualizing smaller part of image with 3D window If some small part of the image needs to be visualized the easiest way is to move the focal point cross of 2D windows to centre of the area of interest Then the centre of 3D window always points towards area of interest After this its easy to zoom and rotate 3D camera around area of interest 2 4 Cut modes Usually the smaller regions are inside the image so that other voxels are between camera and area of interest blocking the view Cut methods are methods for making these blocking voxels invisible Cut modes are found from top left corner of 3D window 2 5 Custom 2D slice directions instead of tansaxial coronal and sagittal By default Carimas visualizes all images in transaxial sagittal and coronal 2D windows Projection View It is also possible to define custom slice directions for 2D visualization Custom slice directions are defined with 3D camera and the three 2D window cuts will be Camera right Camera top and Camera back 2D visualization mode is changed from menu View gt Camera View 3 Segmentation of loaded images Image segmentat
26. ped in an attempt to provide economical storage rapid retrieval of images access to images acquired with multiple modalities and simultaneous access at multiple sites Electronic images and reports are transmitted digitally via PACS parametric image an image that represent both spatial distribution and quantification of the physiological parameters of tracer kinetics pixel short for picture element a single point in a graphics image the smallest element that a device can display and out of which the displayed image is constructed plane The plane is one aspect of an image s matrix The plane indicates where the image is located relative to the patient s position in the scanner gantry When a patient is placed in the gantry head first plane numbers increase in an inferior direction plug in a computer program that can or must interact with another program to provide a certain usually very specific function Typical examples are plugins to display specific graphic formats e g SVG if the browser doesn t support this format natively to play multimedia files to encrypt decrypt email e g PGP or to filter images in graphic programs The main program a web browser or an email client for example provides a way for plugins to register themselves with the program and a protocol by which data is exchanged with plugins 38 polar plot a schematic representation of myocardium of left ventricle in the form of a segmented
27. rain Mirror 18 4 Analysis of segmented regions 4 1 Images we analyse roughly are either static or dynamic as the name implies the critical difference between them is a time dimension Static akin to a photo picture will have one frame dynamic akin to a video will have more than one frame Analysis pathways of static and dynamic images differ Static image analysis In the analysed image the ROI Set consisting of three ROIs has been drawn in the right putamen Edit VOl Next ROI Trace Putamen_1 Tra Putamen 2 Tra Putamen 3 Tra The spherical VOI has been created placed into the region of the left putamen and moulded in three projections with the Vertex tool to assume the shape of the putamen Putamen L V lsphere Putamen R R File gt Edit New gt 19 Click the Analyse tab to enter the analysis mode In the Regions panel you see all VOIs and ROIs present in the image pe L Putamen L V lsphere F C Putamen R ROlset In the right part of the program window the Statistics of selected regions table template will appear The statistics you will get are Mean activity in the region will be in units of the image SD Min Max values the number of Voxels analysed and the Volume of the region Statistics Of Selected Regions For Image PET brain image p utamen L VOlephere utamen R ROlset In the Statistics table you immediately get
28. taining the DICOM slices ca CF WINDOWS system32 cmd exe Co Carimas Larimaz Image uv_ Images on PACS can also be opened from command line with parameter with following syntax PACS SERVER AR StudvInstanceurD SeriesinstanceuTb ca CO WINDOWS system32 cmd exe C Carimas gt Carimas P S BERUERAE 1 2 84H 12494339 1 2 84H 179412839 Orders Carimas to load AE of a Study instance UID Series instance UID images from PACS server 1 4 Viewing the image header A header of a loaded image can be seen from menu View Header or clicking image from image list and selecting Show image header Following dialog is shown Image which header is currently shown Header information used freguently In x Image information R 256 256 112 D M Paterntifame CT reference File Mame CiCarimazsProjectssiCT 22 1 2refdkd ODO0 Patient ID 05143 14310 Dimensions 296x256x112 image ts static tudy Desc MPI Voxel Size 0 7929599881 17218 x 0 79295996811 7218 x 1 249956010698 Series Date 20030627 Series OR Header Items Frame Time Information p T ee rs Serre ation Mame NTECAN Sort Tags By O008 1030 Study Description MPI Number Name Value OO08 103e Series Description NULL n Manufacturer Hode Hamne n y atera E 0008 1140 Da rence are 1 Header tags in tree hierarchy Sorting mode for Sequence 2 PAS ROE header tags OUTS eferenta TF stance UID 1 3 48 PTTSFW 5
29. the values for that region As in the example each VOI will produce one mean value and the corresponding Statistics Statistics Of Selected Regions For Image PET brain image Mean Deviation T Value mm 3 gt Putamen L V lsphere 10 91 25 981 1480 8 When you analyse a ROI set you can get the averaged value for the set as well as values for each of the ROIs drawn p S pan el r aa O Putamen R_ROL1 je H n R RLZ ee HE n R ROLLS Statistics Of Selected Regions For Image PET brain image standard Minimum Maximum o E Voxes bo Putamen L VOlsphere 936 3 046 108 25981 818 14808 Putamen R ROlset se ee jee aw fer 1261 8 Putamen R ROlset Putamen R ROI 2 z Right click on the Regions panel to select or unselect all regions in the panel Select All 4 2 Dynamic image analysis When your main image is a dynamic one click the Analyse tab to get the dynamic analysis view Curve analysis can be performed in three steps File Edit View Image Tools Help Basin Eda PU AA akej splays all the TACs of the project 1 Switch to the Analyz e tab s are calculated from Mask of YOls an change when Ols are modified isNitted to a TAC its name will be displayed at the TAC s name 60 000 40 0 0 0 0 2 Select curves from T T the TAC list DAC egmer Pehor 0 M 08 i 16 TACs Fom ail the f a S f Valugk Of Selected TACs SaveToTXT SaveToDFT A M Cube Tube
30. ts file has RES extension it is in the ASCII format and can be opened by any program opening ASCII files WordPad Word Excel etc TXT Saving the time activity curve was described earlier Reporting Carimas has view for showing patient information and dynamic analysis Summary in one page report This view is shown by selecting report tab 30 Reports of Carimas can be saved only as bitmap and printed Carimas will print the report as landscape and fitted to full page This is done with Print Report and Save as Bitmap buttons when report tab is selected I White Background W Show Plot Print Report save Az Bitmap 31 6 Administration 6 1 Local computer settings PACS server list PACS search field list and colour schemes are personal settings of the user and are saved under users log in the user account Personal i e local settings can be found in the Local Settings tab in the Settings Panel which can be opened from Tools Settings 30 YOI mesh Filters or clicking the Settings button File Edit View Image Took Help lox Project Settings Local Settings Show Dynamic Images With One Frame as Static Dicom Hosts PACS search fields Window Flips Transaxial X Y Z Sagittal x CY Z Coronal Cx DY CZ 6 1 1 Configuring PACS server list Servers can be added and removed dynamically from DICOM host panel that opens by clicking the Dicom Hosts button
31. z l3 2161055210 105670ll 2 6872Z10 Sequence 3 00S 1140 Fefere is zeItzm Toool b 1 Header tag name Header tag value oggie etween F 88 the Tag SPI F Belease L 1S shown 1n red r header tag view ee and image frame time view The image frame time view lists start mid end and duration values for each frame 1 5 Preparing loaded images for visualization 1 5 1 Main and Background images The loaded image in Carimas can be in four qualities main invisible background and selected either main or background Simultaneously you can visualize two images at maximum One will always be the Main image and the other the Background image Click on the image to open the sub menu where you can change the image status Load Segment Analyze J Report ARa JEN O i Bac kground 1 M Tr A To MainImage To Invisible move From List Image status is displayed in parenthesis before image name 1 5 2 The Selected image The Selected image is either the main image or the background one This selection will define the display of colour and frame options Img Slide suma Gray Advanced Radio buttons help switch between Information on frames and colour the Main and Background images are always displayed for the Main Also the colour bar on the right side of all the four windows is the bar for the selected image 1 5 3 Flipping image data
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