1 line
387 KiB
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1 line
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for your Deploy Preview? - Deploy Preview for Viewer\nIntroduction\nThe Open Health Imaging Foundation is developing an open source framework for constructing web-based medical imaging applications. The application framework is built using modern HTML / CSS / JavaScript and uses Cornerstone at its core to display and manipulate medical images. It is built with Meteor, a Node.js-based full-stack JavaScript platform.\nThis documentation concerns the OHIF framework itself and its three example applications: the OHIF Viewer, Lesion Tracker, and the Standalone Viewer.\nThe OHIF Viewer: A general purpose DICOM Viewer (demo)\n\nThe Open Health Imaging Foundation intends to provide a simple general purpose DICOM Viewer which can be easily extended for specific uses. The primary purpose of the OHIF Viewer is to serve as a testing ground for the underlying packages and the Cornerstone family of libraries.\nLesion Tracker: An oncology-focused imaging application (demo)\n\nThe Lesion Tracker is designed to facilitate quantitative assessments of tumour burden over time. It is similar in scope to the ePAD Imaging Platform (https://epad.stanford.edu/), developed at Stanford Medicine.\nStudy List & DICOM Connectivity\n\nThe solution provides a study list and other resources for connecting to PACS and other Image Archives through standard communication approaches (DICOM Web, DICOM Messages).\nStandalone Viewer (demo)\nThe Standalone Viewer offers only the client-side portions of the OHIF Viewer with the Study List pages removed. This single-page viewer can be hosted as a static site (e.g. on Amazon S3, Azure Blob Storage, or Github Pages), and easily integrated with existing back-end DICOM storage systems. Alternative Cornerstone Image Loaders can be included to allow your viewer to support non-DICOM objects (e.g. PNG, JPEG).\n"},"essentials/installation.html":{"url":"essentials/installation.html","title":"Installation","keywords":"","body":"Installation\nGetting the Code\nEither clone the repository using Git:\ngit clone git@github.com:OHIF/Viewers.git\n\nor Download the latest Master as a ZIP File.\nSet up a DICOM server\n\nChoose and install an Image Archive\nUpload some data into your archive (e.g. with DCMTK's storescu or your archive's web interface)\nKeep the server running\n\nOpen Source DICOM Image Archive Options\n\n\n\nArchive\nInstallation\n\n\n\n\nDCM4CHEE Archive 5.x\nInstallation with Docker\n\n\nOrthanc\nInstallation with Docker\n\n\nDICOMcloud (DICOM Web only)\nInstallation\n\n\nOsiriX (Mac OSX only)\n\n\n\nHoros (Mac OSX only)\n\n\n\n\nFeel free to make a Pull Request if you want to add to this list.\nSet up and test the OHIF Viewer (or LesionTracker) application:\n\nInstall Meteor\nOpen a new terminal tab in one of the Application directories (OHIFViewer or LesionTracker)\nInstruct Meteor to install all dependent NPM Packages\nMETEOR_PACKAGE_DIRS=\"../Packages\" meteor npm install\n\n\nRun Meteor using one of the available configuration files.\nMETEOR_PACKAGE_DIRS=\"../Packages\" meteor --settings ../config/orthancDICOMWeb.json\n\nNote: On Windows, you may need to set PACKAGE_DIRS=\"../Packages\" in your Environment Variables in your operating system settings.\n\nLaunch the OHIF Viewer / Lesion Tracker Study List by visiting http://localhost:3000/ in a web browser.\nIf everything is working correctly, you should see the Study List from your archive when you visit the Study List.\n\nDouble-click on a Study in the Study List to launch it in the Viewer\nIf everything is working correctly, you should see your study load into the Viewer.\n\n\nTroubleshooting\n\nIf you receive a \"No Studies Found\" message and do not see your studies, try changing the Study Date filters to a wider range.\nIf you see any errors in your server console, check the Troubleshooting page for more in depth advice.\n\n"},"essentials/getting-started.html":{"url":"essentials/getting-started.html","title":"Getting Started","keywords":"","body":"Getting Started\n...\n"},"essentials/architecture.html":{"url":"essentials/architecture.html","title":"Architecture","keywords":"","body":"Architecture\nMeteor\nMeteor is built on top of Node.js, adding reactive templates (Blaze), a publish/subscribe mechanism (via WebSockets and the Distributed Data Protocol, and a fully integrated client-server MongoDB making it easy to create reactive data elements in the UI.\nStructure of an OHIF Application\nThe OHIF Framework is built as a set of small Meteor packages which can be included as necessary in the final application. Since the logic and templates are largely pushed into packages, the actual application-specific code for each Viewer is relatively short.\nIn brief, to create a new Viewer application, you need to:\n\nDefine the existing pages and the routes which will lead to them\nDefine the overall application layout\nInclude child templates from the OHIF Packages into your application layout\nSpecify desired template options as necessary (e.g. which tools should appear in the toolbar)\n\nUser interface components for your application can be defined in any View layer supported by Meteor (Officially: Angular, React, Blaze, Unofficially: Vue).\n"},"essentials/configuration.html":{"url":"essentials/configuration.html","title":"Configuration","keywords":"","body":"Configurations\nThere are a few pre-defined settings files that you can find in config folder. These are Meteor files and all settings can be accessed as showed on Meteor Website. UI settings are also available as OHIF.uiSettings. See the schema for more information.\nServer settings\n\ndropCollections (boolean): the server will drop all Mongo collections when it's set to true as soon as it has finished starting. This is useful for demo and development environments.\n\nUI Settings\n\nstudyListDateFilterNumDays (integer): define the default date filter (range) on study list. If it's 02/15/2017 and this config is set to 5 then it will search for studies between 02/10/2017 and 02/15/2017.\n\n"},"essentials/troubleshooting.html":{"url":"essentials/troubleshooting.html","title":"Troubleshooting","keywords":"","body":"Troubleshooting\nCommon Problems\n\n\n\nProblem\nMost Common Reasons\n\n\n\n\n Can't retrieve Study List over DICOMWeb\n1. QIDO root URL is incorrect 2. DICOM Web is not enabled on PACS\n\n\n Can't retrieve Study List over DIMSE\n1. PACS is not configured to allow connections from OHIF Meteor Server\n\n\n Can't retrieve images\n1. WADO Root URL is incorrect 2. DICOM Web is not enabled on PACS 3. HTTP Basic Authentication username and password are incorrect or not provided.\n\n\n\nDebugging Steps\nCan't retrieve Study List over DICOMWeb\n\nCheck that you can query your PACS using an alternative DICOM Web client (e.g. cURL, or a Web Browser). If you cannot, then your PACS is configured incorrectly. Refer to the documentation of the image archive.\n2.\n\nCan't retrieve Study List over DIMSE\nCan't retrieve images\n"},"connecting-to-image-archives/options.html":{"url":"connecting-to-image-archives/options.html","title":"What are my options?","keywords":"","body":"Connecting to Image Archives\nWe support DIMSE and DICOMWeb. Which one to use is up to you and depends on your PACS system. DICOMWeb requires no setup on the PACS-side whatsoever, whereas DIMSE may require you to add the 'OHIFDCM' aeTitle to the known DICOM Modalities of your Archive. This is the case for Orthanc, for example (See https://github.com/OHIF/Viewers/wiki/Orthanc-with-DIMSE).\n"},"connecting-to-image-archives/dicomweb.html":{"url":"connecting-to-image-archives/dicomweb.html","title":"DICOM Web","keywords":"","body":"DICOM Web\nDICOMWeb refers to RESTful DICOM Services and is a recently standardized set of guidelines for exchanging medical images and imaging metadata over the internet. Not all archives fully support it yet, but it is gaining wider adoption.\n"},"connecting-to-image-archives/dimse.html":{"url":"connecting-to-image-archives/dimse.html","title":"DICOM Message Service Element","keywords":"","body":"DICOM Message Service Element\nDIMSE Stands for DICOM Message Service Element and is the standard method through which DICOM archives communicate. We support this messaging standard for the retrieval of study, series, and instance metadata because it is widely support. For certain PACS systems, it also (currently) provides faster query results than DICOMWeb.\n"},"connecting-to-image-archives/dcm4chee-with-docker.html":{"url":"connecting-to-image-archives/dcm4chee-with-docker.html","title":"dcm4chee w/ Docker","keywords":"","body":"DCM4CHEE with Docker\n\nInstall Docker (https://www.docker.com/)\nFollow the DCM4CHEE Guidelines for Running on Docker.\n The easiest path is to use Docker-Compose which will start and stop multiple containers for you. There are excellent instructions provided by the DCM4CHEE team on the 'light archive' repository:\n https://github.com/dcm4che/dcm4chee-arc-light/wiki/Running-on-Docker#use-docker-compose\n\nCreate docker-compose.yml and docker-compose.env files\nStart the containers:\ndocker-compose start\n\nNote: If you are running this on Mac OSX you will probably need to change the default docker-compose.yml file slightly. Specifically, the paths that refer to /var/local/ will likely need to be changed to /opt/\n\n\n\nRun the OHIF Viewer or Lesion Tracker using the dcm4cheeDIMSE.json configuration file\n\n\ncd OHIFViewer\nPACKAGE_DIRS=\"../Packages\" meteor --settings ../config/dcm4cheeDIMSE.json\n\nWeb Service URLs from DCM4CHEE:\nOriginal source here: https://github.com/dcm4che/dcm4chee-arc-light/wiki/Running-on-Docker#web-service-urls\n\n\nArchive UI: http://localhost:8080/dcm4chee-arc/ui - if secured, login with\n Username | Password | Role\n --- | --- | ---\n user | user | user\n admin | admin | user + admin\n\nKeycloak Administration Console: http://localhost:8080/auth, login with Username: admin, Password: admin.\nWildfly Administration Console: http://localhost:9990, login with Username: admin, Password: admin.\nKibana UI: http://localhost:5601\nDICOM QIDO-RS Base URL: http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs\nDICOM STOW-RS Base URL: http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs\nDICOM WADO-RS Base URL: http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs\nDICOM WADO-URI: http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/wado\n\n\n"},"connecting-to-image-archives/orthanc-with-docker.html":{"url":"connecting-to-image-archives/orthanc-with-docker.html","title":"Orthanc w/ Docker","keywords":"","body":"Orthanc with Docker\nDepending on whether or not you want uploaded studies to persist in Orthanc after Docker has been closed, there are two different methods for starting the Docker image:\nTemporary data storage\nThis command will start an instance of the jodogne/orthanc-plugins Docker image. All data will be removed when the instance is stopped!\ndocker run --rm -p 4242:4242 -p 8042:8042 jodogne/orthanc-plugins\nPersistent data storage\nIn order to allow your data to persist after the instance is stopped, you first need to create an image and attached data volume with Docker. The steps are as follows:\n\nCreate a persistent data volume for Orthanc to use\n docker create --name sampledata -v /sampledata jodogne/orthanc-plugins\n Note: On Windows, you need to use an absolute path for the data volume, like so:\n docker create --name sampledata -v '//C/Users/erik/sampledata' jodogne/orthanc-plugins\n\nRun Orthanc from Docker with the data volume attached\n docker run --volumes-from sampledata -p 4242:4242 -p 8042:8042 jodogne/orthanc-plugins\n\nUpload your data and it will be persisted\n\n\n"},"connecting-to-image-archives/osirix.html":{"url":"connecting-to-image-archives/osirix.html","title":"Osirix","keywords":"","body":"Example: Osirix\n...\n"},"data/data-hierarchy.html":{"url":"data/data-hierarchy.html","title":"Data Hierarchy","keywords":"","body":"Data Hierarchy\nStudies, Series, Instances, Frames\nDisplay Sets\n"},"data/image-viewport.html":{"url":"data/image-viewport.html","title":"Image Viewport","keywords":"","body":"Image Viewport\nMain Viewport Component\nThe imageViewerViewport component\n"},"layout/layout-management.html":{"url":"layout/layout-management.html","title":"Layout Management","keywords":"","body":"Layout Management\n"},"layout/hanging-protocols.html":{"url":"layout/hanging-protocols.html","title":"Hanging Protocols","keywords":"","body":"Hanging Protocols\n"},"packages/measurements.html":{"url":"packages/measurements.html","title":"Measurements Package (ohif-measurements)","keywords":"","body":"Measurements Package (ohif-measurements)\nPackage design\nUsage\nHow to define a Measurement tool\nHow to validate Measurements\nData exchange concepts\nLongitudinal Measurements\nTimepoints\n"},"deployment/building-for-production.html":{"url":"deployment/building-for-production.html","title":"Building for Production","keywords":"","body":"Building for Production\nThis tutorial considers the current folder as OHIFViewer/.\nDependencies\nFirst, you need to have installed:\n\nNode.js and NPM\nMeteor\nMongoDB\n\nMongoDB is actually not required if you have a remote MongoDB. If your database is local then you need to have it running.\nCheck your packages\nInside of the viewer folder make sure NPM packages are updated for production:\nnpm install --production\n\nBuilding\nThere are two ways of building OHIF Viewer for a specific DICOM server: Automatically or Manually.\nFor both, we use the meteor build (check it's docs) app and Orthanc Dicom Web Server.\nFor meteor build it's necessary to inform an output folder myOutputFolder.\nRemember to change myOutputFolder to your folder location.\nOHIF Viewer will be built using Orthanc DICOM Web server configuration file ../config/orthancDICOMWeb.json to set METEOR_SETTINGS environment var.\nTo run with another server, just point to the corresponding .json located in config folder or create your own.\nBuild automatically\nAfter this step, go directly to Prepare to run production build.\nNon-windows users\nMETEOR_PACKAGE_DIRS=\"../Packages\" METEOR_SETTINGS=$(cat ../config/orthancDICOMWeb.json) meteor build --directory myOutputFolder\n\nWindows users\nSince there is no cat command in Windows cmd, use Windows PowerShell (at least version 3.0) instead.\nIn PowerShell, open a new shell as an admin:\nStart-Process powershell -Verb runAs\n\nThen:\nRemember to change OHIFViewerFolderLocation to OHIFViewer's folder location.\ncd OHIFViewerFolderLocation\n$settings = Get-Content ..\\config\\orthancDICOMWeb.json -Raw\n$settings = $settings -replace \"`n\",\"\" -replace \"`r\",\"\" -replace \" \",\"\"\n[Environment]::SetEnvironmentVariable(\"METEOR_SETTINGS\", $settings, \"Machine\")\nSET METEOR_PACKAGE_DIRS=\"../Packages\"\nmeteor build --directory myOutputFolder\n\nBuild manually\nOHIF Viewer will be built normally, but with no DICOM Server information, which needs to be added when running the build. This is described in Manually adding DICOM Server to the Viewer.\nNon-windows users\nMETEOR_PACKAGE_DIRS=\"../Packages\" meteor build --directory myOutputFolder\n\nWindows users in cmd\nSET METEOR_PACKAGE_DIRS=\"../Packages\"\nmeteor build --directory myOutputFolder\n\nPrepare to run production build\nIf everything went ok, meteor build created a bundle folder inside myOutputFolder.\nRemember to change myOutputFolder to your folder location.\nGo to that folder:\ncd myOutputFolder/bundle\n\nNow install the NPM dependencies:\ncd programs/server\nnpm install\n\nTo run production build\nGo back to the bundle folder:\ncd ../..\n\nor (Remember to change myOutputFolder to your folder location.):\ncd myOutputFolder/bundle\n\n3 environment variables are set before running Node.js:\n\nMONGO_URL: is the url to MongoDB. If it's local, you need to have it running\nROOT_URL: the hostname where you can access your Viewer in the browser\nPORT: the port the Viewer will run\n\nThis way, the Viewer can be accessed in http://localhost:3000, with MongoDB running locally using 27017 port (it's default).\nNon-windows users\nMONGO_URL=mongodb://localhost:27017/myapp ROOT_URL=http://localhost PORT=3000 node main.js\n\nWindows users in cmd\nSET MONGO_URL=mongodb://localhost:27017/myapp\nSET ROOT_URL=http://localhost\nSET PORT=3000\nnode main.js\n\nManually adding DICOM Server to the Viewer\nIf DICOM Server was configured automatically during the building process, skip this step.\nAccess the viewer http://localhost:3000 and toggle the Options menu, located at top right corner. Select Server Information option.\nIn Server Information dialog click on Add a new server button and fill the fields accordingly to the DICOM Server to be added.\nIn case of doubts about any field in this dialog, use config/orthancDICOMWeb.json as reference.\nAfter filling the form, click on the Save button and the new server will be listed. Make sure to activate it by clicking on the left most button (a checkbox button) in the Actions column.\nRefresh the page and Viewer will be connected to the DICOM Server.\n"},"deployment/security.html":{"url":"deployment/security.html","title":"Security","keywords":"","body":"Security\n"},"I-want-to/add-a-tool-to-the-viewer.html":{"url":"I-want-to/add-a-tool-to-the-viewer.html","title":"Add a Tool to the Viewer","keywords":"","body":"Add a Tool to the Viewer\nTo add a tool to the Viewer there are a few steps:\n\nAdd the tool itself to the repository.\nIf you're using something from Cornerstone Tools you can skip this step.\nSome examples of custom tools can be found in the lesion tracker: https://github.com/OHIF/Viewers/tree/master/Packages/ohif-lesiontracker/client/compatibility\n\nAdd the toolbar button itself to the array of tools in the Toolbar:\nhttps://github.com/OHIF/Viewers/blob/574a6d02b090b8b2f020430c5919f8377b8316c6/OHIFViewer/client/components/toolbarSection/toolbarSection.js\n\nA: Add it to the toolManager (if it's a tool, such as length / angle):\nhttps://github.com/OHIF/Viewers/blob/574a6d02b090b8b2f020430c5919f8377b8316c6/Packages/lesiontracker/client/tools.js#L2\n --- OR --- \nB: Add it to the functionList if it's a command (e.g. toggle CINE play, or Invert the current viewport):\nhttps://github.com/OHIF/Viewers/blob/574a6d02b090b8b2f020430c5919f8377b8316c6/OHIFViewer/client/components/viewer/viewer.js#L12\n\n\n"},"I-want-to/add-a-logo-to-the-viewer.html":{"url":"I-want-to/add-a-logo-to-the-viewer.html","title":"Add a Logo to the Viewer","keywords":"","body":"Add a Logo to the Viewer\nThe OHIF Framework provides ohif-header package to add a header into application layout. ohif-header package is designed as a custom block helper named header to define your own header context.\nIf you would like to add SVG logo to header please follow these steps.\n\nAdd your SVG logo into public folder.\n\nAdd header content block which will be located on the top of the application layout into your application's main template. You can also pass some parameters to header content block to customize the header.\n\nheaderClasses: the list of classes which will be applied to header element\nbrandHref: the url of the logo to link\n\n\n\n{{#header headerClasses=\"header-big bg-blue\" brandHref=\"your logo link\"}}\n...\n{{/header}}\n\n\nCreate a section called as brand in header content block and add your logo content which is displayed on the left side of the header as default into section brand.\n\n {{#header}}\n {{#section \"brand\"}}\n \n \n \n \n\n \n Logo Text\n {{/section}}\n {{/header}}\n\n For example, see how it works in OHIF Viewer\n"},"example-applications/ohif-viewer.html":{"url":"example-applications/ohif-viewer.html","title":"OHIF Viewer","keywords":"","body":"OHIF Viewer\n"},"example-applications/lesion-tracker.html":{"url":"example-applications/lesion-tracker.html","title":"Lesion Tracker","keywords":"","body":"Lesion Tracker\n"},"example-applications/standalone-viewer.html":{"url":"example-applications/standalone-viewer.html","title":"Standalone Viewer","keywords":"","body":"Standalone Viewer\n"},"standalone-viewer/usage.html":{"url":"standalone-viewer/usage.html","title":"Usage","keywords":"","body":"Standalone Viewer\nQuick Start\nInstall dependencies:\nmeteor npm install\n\nRun the application:\nMETEOR_PACKAGE_DIRS=\"../../Packages\" ROOT_URL=http://localhost:3000 meteor\n\nOpen your web browser and navigate to one of the following URLs to test the standalone viewer application:\nhttp://localhost:3000/testId\n\nOr, to load DICOMs:\nhttp://localhost:3000/testDICOMs\n\nTo Build for the Client\nIt is possible to build this standalone viewer to run as a client-only bundle of HTML, JavaScript, and CSS.\n\nFirst, install meteor-build-client-fixed.\nsudo npm install -g meteor-build-client-fixed\n\n\nNext, build the client bundle into an output folder (\"myOutputFolder\") with a base URL (\"localhost:3000\"). In production, this would be the URL where the Viewer is available.\nMETEOR_PACKAGE_DIRS=\"../../Packages\" meteor-build-client-fixed ../myOutputFolder -u localhost:3000\n\nTest the bundled client-side package locally.\n Note: You will need to have Python installed to run the test server for this case. It is not a typical simple HTTP server. The bundled script redirects all URLs following the base URL to index.html. It will then use the routes defined in your application to handle the URL parameters.\n In our case, this means it will request a JSON file at baseURL/api/[id parameter].\n So if you navigate to http://localhost:3000/sampleJPEG.json the application will retrieve the JSON from http://localhost:3000/api/sampleJPEG.json and use it to populate the viewer. If something appears to be broken, make sure you retrieve a JSON file at the /api URL.\n Create the api folder for your data\ncd myOutputFolder\nmkdir api\n\n Copy your data into the folder\ncp ../etc/sample* api/\n\n Run the server\npython ../etc/redirectingSimpleServer.py\n\n Open your web browser and navigate to http://localhost:3000/sampleJPEG.json or http://localhost:3000/sampleDICOM.json\n\n\nTesting the Sample client-only build\nFor the sake of simplicity we have also included a pre-built client-only version of the standalone viewer, which can be found in the SampleClientOnlyBuild folder.\nYou can test this with:\n cd SampleClientOnlyBuild\n python ../etc/redirectingSimpleServer.py\n\n"},"lesion-tracker/user-manual.html":{"url":"lesion-tracker/user-manual.html","title":"User Manual","keywords":"","body":"Lesion Tracker - User Manual\n\nInstallation on Windows\nManage Studies in Orthanc\nUser Accounts\nStudy and Timepoint Management\nLesion Tracking\nUser Preferences\nServer Management\nAudit Trail\n\n"},"lesion-tracker/installation-on-windows.html":{"url":"lesion-tracker/installation-on-windows.html","title":"Installation on Windows","keywords":"","body":"Lesion Tracker - Installation on Windows\nOn Windows, the easiest way to install LesionTracker is using the provided Windows Installer. You can download the latest version of LesionTracker installer from OHIF\nInstall\n\nAfter you have obtained the latest version of LesionTracker installer, double-click the installer to install the application.\nWhen you start the installer, setup wizard will pop up.\n\n\nClick Install to start the installation.\n\nLesionTracker will install prerequisites if they do not exist before installing the application.\n\n\nClick the Next if you accept the installation.\n\n\nRead the license agreement, and if you agree, click I accept the terms in the License Agreement and then click the Next.\n\n\nSelect a location to install LesionTracker and click the Next to continue.\n\n\nClick the Install to start the installation and the installation will be started.\n\n\nClick Finish to complete the installation.\n\n\nWhen the installation is done,\n\nYou will see the final dialog which gives the URLs in order to connect to LesionTracker Viewer and Orthanc Server.\n\nIt will launch computer's default browser and display LesionTracker Viewer if you click 'http://localhost:3000'\nIt will launch computer's default browser and enables to upload studies to Orthanc Server if you click 'http://localhost:8042'\n\n\n\nAlso, LesionTracker installer will create two shortcuts named LesionTracker and Orthanc Server on the Desktop.\n\nIt will launch computer's default browser and display LesionTracker image viewer if you click LesionTracker application on the Desktop.\nIt will launch computer's default browser and enables to upload studies to Orthanc Server if you click Orthanc Server application.\n\n\n\nClick the Done and Close to close the installation window.\n\n\nAfter the installation is completed,\n\nYou can find the project folder in C:\\Program Files\\OHIF\\LesionTracker if you use the default installation location.\nYou will find 4 program executables which eases managing the services in the project folder:\n\nStart Services.exe: Starts LesionTracker, MongoDB and Orthanc services manually.\nStop Services.exe: Stops LesionTracker, MongoDB and Orthanc services manually.\nTurn Off Auto Services.exe: Configures not to start LesionTracker, MongoDB and Orthanc services automatically when Windows starts up.\nTurn On Auto Services.exe: Configures to start LesionTracker, MongoDB and Orthanc services automatically when Windows starts up.\n\n\n\n\nUninstall\n\nOpen the Start Menu.\nClick Settings.\nClick Apps on the Settings menu.\nSelect Apps & features from the left panel.\nFind the LesionTracker in programs list and click LesionTracker, then click the Uninstall.\n\n\nClick Uninstall from the LesionTracker Setup dialog.\n\n\n\nWhen the uninstallation is done, the uninstallation will remove;\n\nPrerequisites: MongoDB, nodejs and Orthanc Server\nThe project folder, OHIF, from C:\\Program Files\nBackground Services: LesionTracker Server, MongoDB and Orthanc services\nShortcuts: LesionTracker and Orthanc Server shortcuts on the Desktop\n\n"},"lesion-tracker/manage-studies-in-orthanc.html":{"url":"lesion-tracker/manage-studies-in-orthanc.html","title":"Manage Studies in Orthanc","keywords":"","body":"Lesion Tracker - Manage Studies in Orthanc\nOrthanc is an open-source, simple and powerful standalone DICOM server which eases DICOM scripting and data management for clinical routine and medical research. LesionTracker installer installs Orthanc as a service and runs automatically in the background. Orthanc serves a web interface, Orthanc Explorer, and it can be accessed through http://localhost:8042 in your web browser or the Orthanc Server shortcut which is created by LesionTracker installer and loads http://localhost:8042 in your default browser.\nUpload a study into Orthanc using Orthanc Explorer\n\nClick Upload button at the top-right of Orthanc Explorer and you will be brought to the upload page.\n\n\nSelect the DICOM files and drag those files into Orthanc Explorer.\n\n\nClick Start the upload and wait until the upload is complete.\n\n\nClick Patients to view the uploaded study.\n\n\n\nDelete a study from Orthanc using Orthanc Explorer\n\nSelect a patient from Patients list.\n\n\nSelect a study of the patient.\n\n\nSelect Delete this study in the Interact menu.\n\n\n\n"},"lesion-tracker/user-accounts.html":{"url":"lesion-tracker/user-accounts.html","title":"User Accounts","keywords":"","body":"Lesion Tracker - User Accounts\nSign In\nLesionTracker requires authentication to access the viewer.\nIf you are already a registered user, enter Your Email and Password and click Sign In\n\nRegister An Account\nIf you are a new user, click Need An Account and fill the all fields and click Join Now\n\nNote: There is a Test Drive button on the top-right of Login page. Test Drive is used to skip registration process and allows to use LesionTracker with a test account. This will be removed in the next versions.\nForgot Password\nTo reset the password, enter Your Email and click Send Reminder. An email that includes a link to reset your password will be sent to your email address.\n\nChange Password\nTo change password:\n\nClick Configuration menu icon at the top-right of the workspace then select Change Password\nEnter your password and click Change Password\n\n\nLogout\nTo logout, click Logout on the Configuration menu.\n\n"},"lesion-tracker/study-and-timepoint-management.html":{"url":"lesion-tracker/study-and-timepoint-management.html","title":"Study and Timepoint Management","keywords":"","body":"Lesion Tracker - Study and Timepoint Management\n\n\nStudy List allows to sort each column. To sort studies, click the desired column header.\nStudy List is filterable for each column and you can filter by more than one column by typing in the column field. To filter a column, type the text in the desired column header field and press Enter.\nPagination is provided for the Study List at the bottom of the page. You can change the number of rows per page or the current page.\n\nStudy List Context Menu\nWhen you right-click on the study row, Study Context Menu will pop up. Study Context Menu includes operations at the study level.\nThere are a couple of ways to view a study:\n\nSimply double-click on the study row.\nSelect View option on the Study Context Menu, then you will be redirected to Viewer page.\n\n\nTimepoint Association\n\nTo link a study with a timepoint, right-click on the study row and select Associate option on the Study Context Menu. You will see Study Association dialog.\nTo link multiple studies at the same time, hold Shift key and select studies you would like to associate, then right-click and select Associate on the Study Context Menu\n\n\nThe Study Association dialog allows you to select and unselect Timepoint Type for the selected study or studies. Also, it will include all studies within 14 days of your selected studies, in case you forgot to select a study. After you identify timepoints for the selected study or studies, click Save to save the association.\n\nRemove Timepoint Association\nTo unlink a timepoint association with a study, right-click on the study row and select Remove Association option on the Study Context Menu. Remove Association will be disabled if the study is already dissociated.\n\nView Series Details\nTo view details of related series, right-click on the study row and select View Series Details option on the Study Context Menu, then Series Details dialog will pop up. Series Details dialog gives a summary of the selected study.\n\nAnonymize (Under Development)\n...\nSend (Under Development)\n...\nExport (Under Development)\n...\nDelete (Under Development)\n...\n"},"lesion-tracker/using-the-viewer.html":{"url":"lesion-tracker/using-the-viewer.html","title":"Using the Viewer","keywords":"","body":"Lesion Tracker - Using the Viewer\nAfter you double-click a study, the Lesion Tracking imaging application will be launched. The basic patient and study data is displayed in the Image Viewer.\n\nSwitching Studies and Series\nThere are two methods to switch studies and series inside each viewport:\nStudies Panel\nStudies Panel at the left side of the workspace allows you to change studies and series. Click Studies button to toggle Studies Panel. You can view images in two ways:\n\nDouble-click the desired series thumbnail.\nDrag and drop the desired series thumbnail on the image viewer.\n\n\nQuick Switch Tool\nQuick Switch Tool in the top-middle of the workspace allows you to switch studies and series for the active image viewer easily. Selected series will be colored by the theme colors.\n\nImage Manipulation Tools\nImage Manipulation Tools are available in the toolbar at the top of the workspace.\nZoom Tool\nThere are a couple of ways to zoom the image:\n\nSelect Zoom Tool and down on the image with the left mouse button.\nDown on the image the right mouse button without selecting Zoom Tool.\n\n\nWindow Width & Level\nThere are a couple of ways to change the window/level of the image:\n\nSelect Levels Tool and drag on the image with the left mouse button. Dragging up decreases the level and dragging left decreases the window width.\n\n\nAlternatively, you can use default Window/Level Presets which are defined in User Preferences dialog or create your window level values.\n\n\n\nPan Tool\nThere are a couple of ways to pan the image:\n\nSelect Pan Tool and move the image around the screen with the left mouse button.\nMove the image around the screen with the middle mouse button without selecting Pan Tool.\n\n\nStack Scroll Tool\nThere are a number of ways to scroll images:\n\nScroll up and down the mouse wheel.\nDrag the scroll bar at the right side of the image viewer.\nUse Up and Down buttons on the keyboard.\n\n\nLesion Tracking Basics\nView Case Response Criteria\nLesionTracker supports Conformance Checks for RECIST 1.1 and click Trial to view Response Criteria details.\nNote: Trial button is available if the study is associated with a timepoint.\n\nMeasurements Table\nTo view measurements and manipulate the lesions, click Measurements button at the top-right of the workspace. The Measurements table will be displayed at the right side of the workspace. To hide the Measurements the table, click Measurements button.\nNote: Measurements button is available if the study is associated with a timepoint.\n\nTarget Tool\n\nTo create a target, select Target Tool and click on the image.\nHold, drag and release the mouse button to create the target.\n\n\nTo label the target, click Add Label button.\n\n\nTo resize the measurement, hover the mouse over the end points of the target then click and drag.\n\nTo rename the lesion, click the lesion number in the Measurements table then click Rename\n\n\nTo delete the lesion, click the lesion number in the Measurements table then click Delete. It will delete the lesion from the Measurements table and the image.\n\n\n\nCompletely Resolved (CR) Target Tool\nTo make a lesion completely resolved, click Target Tool and select CR Target from Target Tool pop up.\n\nUnknown (UN) Target Tool\nTo mark a lesion as unknown, click Target Tool and select UN Target from Target Tool pop up.\n\nNon-Target Tool\n\nTo create a non-target, select Non-Target Tool and click on the image.\nHold, drag and release the mouse button to create a non-target.\n\n\nSelect Lesion Location and Lesion Location Response then click Confirm.\n\n\nTo resize the measurement, hover the mouse over the end points of the non-target then click and drag.\n\nTo rename the lesion, click the lesion number in the Measurements table then click Rename\nTo delete the lesion, click the lesion number in the Measurements table then click Delete. It will delete the lesion from the Measurements table and the image.\n\nView Lesion\nTo view the lesion on the image, click the measurement record in the Measurements table then the image which includes the lesion will be displayed by activating the selected lesion.\n\nConformance Checks\nAny lesion that will conflict with Response Criteria for RECIST 1.1 will be flagged in the Measurements table. To view criteria non-conformities, click the icon at the left of the lesion record in the Measurements table.\n\nGenerating PDF Reports\n\nTo generate reports of measurements, click Generate Report button at the bottom of the Measurements table.\n\n\n\nA PDF file which includes target and non-target measurements with annotated image snapshots will be created.\n\n\nSaving Measurements\nThere a couple of ways to save changes:\n\nClick Save button at the top-right of the workspace.\n\n\nClick Study list to save changes and go back to Study List.\n\n\n\nTimepoint Comparison\nLesionTracker allows to compare time points and manipulate the measurements on the timepoint images. To launch the compare mode:\n\nAssociate a study with Follow-up timepoint then double-click Follow-up study. Follow-up and Baseline studies will be displayed in 1x2 layout and Baseline study will show the image which includes the first target measurement as default.\nMeasurements in the Follow-up must be created in the same order as they were on Baseline.\n\n\n\nComparison\n Comparison tab in the Measurements table allows you to display lesions in the timepoint compared.\n\nKey Timepoints\nKey Timepoints tab in the Measurements table allows you to display the lesions by the timepoints at the same time.\n\nImage Review\nTo compare the lesions in Baseline and Follow-up, click the lesion record in the Measurements table. The recorded lesions will be displayed on the Baseline and Follow-up images\nStack Scroll Tool**\nTo scroll between two series synchronously, click More button and select Stack Scroll Tool.\n\nCase Progress\nCase Progress icon displays the progress of target and non-target lesions which are assessed out of total lesions. Number in the middle of the icon shows the number of lesions which are not assessed.\n\nHeads Up Display (HUD) Panel\nTo have a quick view of the Measurements table, click HUD button at the top-right of the workspace. You can easily move and resize the HUD Panel on the workspace.\n\nNote: HUD button is only available if the study is associated with a timepoint.\nAdditional Tools\nTemporary Length Measurement\nTo check the size of a lesion without adding to the Measurements table, select Temp Tool.\n\nStack Scroll Tool\nTo scroll images:\n\nClick More button and select Stack Scroll Tool.\nDrag down and up on the image viewer with the left mouse button.\n\n\nReset Image Tool\nTo reset the geometric orientation, position and magnification of the image in the active image viewer, click More button and select Reset Tool.\n\nRotate Right Tool\nTo rotate the image in the active image viewer 90 degree clockwise, click More button and select Rotate Right Tool.\n\nFlip H Tool\nTo flip the image in the active image viewer horizontally, click More button and select Flip H Tool.\n\nFlip V Tool\nTo flip the image in the active image viewer vertically, click More button and select Flip V Tool.\n\nInvert Tool\nTo invert the image in the active image viewer, click More button and select Invert Tool.\n\nMagnify Tool\nMagnify Tool allows to zoom in a part of the image without changing zoom level of the whole image.\n\nClick More button and select Magnify Tool.\nClick and drag around the image with the left mouse button.\n\n\n3.7.9. Ellipse Tool\nEllipse Tool allows you to draw elliptical annotation with mean and standard deviation values.\n\nClick More button and select Ellipse Tool then click on the image.\nHold, move and release the mouse button to create the annotation.\n\n\nSave Screenshot\nTo save a screenshot of the current active viewport:\n\nClick More button and click Save Screenshot.\nSet image name and sizes and click Download.\n\n\nCINE Tool\nCINE Tool allows to play through stacks of images in the active viewport.\n\nClick More button and click CINE Tool. The CINE dialog will pop up.\nClick the desired media options from the CINE dialog.\nTo close CINE dialog, click CINE Tool.\n\n\n"},"lesion-tracker/user-preferences.html":{"url":"lesion-tracker/user-preferences.html","title":"User Preferences","keywords":"","body":"Lesion Tracker - User Preferences\nTo view User Preferences dialog, select Preferences on the Configuration menu. User Preferences dialog includes a couple of tabs:\n\nKeyboard Shortcuts\nThere are a number of default shortcuts for the defined tools. To change the shortcut for the tool, type the desired key into the tool field.\n\nWindow Width & Level Presets\nThere are a number of default Window Width/Level settings in the Window W/L tab. To create a new setting, enter the desired column field.\n\nColor Themes\n\nTo modify the colors in the viewer, select Themes from Configuration menu.\nSelect a theme then click Apply theme to change the theme.\n\n\n"},"lesion-tracker/server-management.html":{"url":"lesion-tracker/server-management.html","title":"Server Management","keywords":"","body":"Lesion Tracker - Server Management\nLesionTracker supports configuration of multiple servers and allows to switch between them. To configure the servers, click Server Information on the Configuration Menu.\n\n"},"lesion-tracker/audit-trail.html":{"url":"lesion-tracker/audit-trail.html","title":"Audit Trail","keywords":"","body":"Lesion Tracker - Audit Trail\n\nTo view Audit Trails, select View Audit Log on the Configuration menu.\nTo filter audit logs for a column or multiple columns, type or select in the related column or columns.\n\n\n"},"faq/general.html":{"url":"faq/general.html","title":"General","keywords":"","body":"Frequently Asked Questions - General\nHow do I file a bug?\nWe accept and triage bug reports through Github primarily.\n\nCreate a Github account\nSearch the current Issue List to ensure you are not creating a duplicate issue.\nIf your issue already exists, post a comment to show us that this issue also affects you.\n\nIf no prior issue exists, Create a New Issue on the repository.\n\n\nSome tips for filing a new issue:\n\nMake sure your issue is reproducible: If we try to reproduce your issue given your provided steps and we cannot reproduce it, we will not be able to fix it. Nobody wants to spend time guessing how to reproduce your issue! Before filing, please reproduce your issue more than once and clearly describe the steps taken.\nIf you are reporting a user interface issue, provide screenshots: A picture is worth a thousand words. If your issue concerns the UI, screenshots will help us identify the issue dramatically faster since it can be extremely challenging to describe UI bugs with text. You should still clearly describe the steps that you took to produce the issue.\nInclude platform & environment: Your operating system, web browser, and web browser version are highly relevant for many bugs. Please provide these with all bug reports.\nInclude expected and actual result: Tell us what you expected to happen, and what actually happened. If you don't do this, we might not consider it a bug.\n\nHow can I request a new feature?\nAt the moment we are in the process of defining our roadmap and will do our best to communicate this to the community. If your requested feature is on the roadmap, then it will most likely be built at some point. If it is not, you are welcome to build it yourself and contribute it. If you have resources and would like to fund the development of a feature, please contact us.\nWho should I contact about Academic Collaborations?\nGordon J. Harris at Massachusetts General Hospital is the primary contact for any academic collaborators. We are always happy to hear about new groups interested in using the OHIF framework, and may be able to provide development support if the proposed collaboration has an impact on cancer research.\nDo you offer commercial support?\nThe Open Health Imaging Foundation does not offer commercial support, however, some community members do offer consulting services. The following contacts may be useful:\n\nRob Lewis (Radical Imaging)\n\nPlease file a Pull Request if you wish to add your name or organization to this list.\nI emailed my question to you directly and you did not respond. Why not?\nEmailing developers directly is not a shortcut to faster support. Please file your issues and questions on Github so that everyone can benefit from the discussion and solutions.\nDo your Viewers have 510(k) Clearance from the U.S. F.D.A or CE Marking from the European Commission?\nNO. The OHIF Viewer, Lesion Tracker, and Standalone Viewer, NOT F.D.A. cleared or CE Marked. It is the users responsibility to ensure compliance with applicable rules and regulations. The License for the OHIF Framework does not prevent your company or group from seeking F.D.A. clearance for a product built using the framework.\nIf you have gone this route (or are going there), please let us know because we would be interested to hear about your experience.\nAre your Viewers HIPAA Compliant?\nNO. The OHIF Viewer, Lesion Tracker, and Standalone Viewer DO NOT fulfill all of the criteria to become HIPAA Compliant. It is the users responsibility to ensure compliance with applicable rules and regulations.\nThe Lesion Tracker application demonstrates some available components and features (e.g. Audit Trail, automatic logoff, and unique user identification for User Accounts) which could be used by third parties seeking HIPAA compliance.\n"},"faq/technical.html":{"url":"faq/technical.html","title":"Technical","keywords":"","body":"Frequently Asked Questions - Technical\nWhy is your framework built with Meteor?\nAt the time of project conception, Meteor was a simple way to begin using bleeding edge web technologies without putting significant effort into configuration and build processes. Although Meteor does have some drawbacks, it remains a simple all-in-one solution.\nDo you have any plans to stop using Meteor?\nWe have considered migrating templates from Blaze (http://blazejs.org/) to React (https://reactjs.org/) or Vue (https://vuejs.org/), simply because these decouple the view layer from the remainder of the application. Blaze currently lacks Stand-alone Support which means that our templates are not re-usable outside of a Meteor application. This is certainly a downside, but the resource cost to migrate every template is significant.\n"},"contributing.html":{"url":"contributing.html","title":"Contributing","keywords":"","body":"Contributing\nI would like to contribute code - how do I do this?\nFork the repository, make your change and submit a pull request.\nAny guidance on submitting changes?\nWhile we do appreciate code contributions, triaging and integrating contributed code changes can be very time consuming. Please consider the following tips when working on your pull requests:\n\nFunctionality is appropriate for the repository. Consider posting on the forum if you are not sure.\nCode quality is acceptable. We don't have coding standards defined, but make sure it passes ESLint and looks like the rest of the code in the repository.\nQuality of design is acceptable. This is a bit subjective so you should consider posting on the forum for specific guidance.\nThe scope of the pull request is not too large. Please consider separate pull requests for each feature as big pull requests are very time consuming to understand.\n\nWe will provide feedback on your pull requests as soon as possible. Following the tips above will help ensure your changes are reviewed.\nTesting contribution pull requests\nOHIF uses netlify so that pull requests are autogenerated and available for testing.\nFor example, this url allows you to test pull request 237, the request that created this FAQ entry, using data pulled from Amazon S3.\nReplacing the number 237 in the link below with your pull request number should let you test it as well and you can use this link for discussions on github without requiring reviewers to download and build your branch.\nhttps://deploy-preview-237--ohif.netlify.com/viewer/?url=https://s3.eu-central-1.amazonaws.com/ohif-viewer/sampleDICOM.json\nIf you have made a documentation change, a link like this will let you preview the gitbook generated by the pull request:\nhttps://deploy-preview-237--ohif.netlify.com/contributing.html\n"}}} |