init
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mario
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{
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"label": "User Guide",
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"position": 2
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}
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83
platform/docs/versioned_docs/version-3.8/user-guide/index.md
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83
platform/docs/versioned_docs/version-3.8/user-guide/index.md
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---
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sidebar_position: 2
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sidebar_label: Study List
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---
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# Study List
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## Overview
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The first page you will see when the viewer is loaded is the `Study List`. In
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this page you can explore all the studies that are stored on the configured
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server for the `OHIF Viewer`.
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## Sorting
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When the Study List is opened, the application queries the PACS for 101 studies
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by default. If there are greater than 100 studies returned, the default sort for
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the study list is dictated by the image archive that hosts these studies for the
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viewer and study list sorting will be disabled. If there are less than or equal
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to 100 studies returned, they will be sorted by study date (most recent to
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oldest) and study list sorting will be enabled. Whenever a query returns greater
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than 100 studies, use filters to narrow results below 100 studies to enable
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Study List sorting.
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## Filters
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There are certain filters that can be used to limit the study list to the
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desired criteria.
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- Patient Name: Searches between patients names
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- MRN: Searches between patients Medical Record Number
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- Study Date: Filters the date of the acquisition
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- Description: Searches between study descriptions
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- Modality: Filters the modalities
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- Accession: Searches between patients accession number
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An example of using study list filter is shown below:
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Below the study list are pagination options for 25, 50, or 100 studies per page.
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## Study Summary
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Click on a study to expand the study summary panel.
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A summary of series available in the study is shown, which contains the series
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description, series number, modality of the series, instances in the series, and
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buttons to launch viewer modes to display the study.
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## Study Specific Modes
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All available modes are seen in the study expanded view. Modes can be enabled or
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disabled for a study based on the modalities contained within the study.
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In the screenshot below, there are two modes shown for the selected study
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- Basic Viewer: Default mode that enables rendering and measurement tracking
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- PET/CT Fusion: Mode for visualizing the PET CT study in a 3x3 format.
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Based on the mode configurations (e.g., available modalities), PET/CT mode is
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disabled for studies that do not contain PET AND CT images.
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<!-- This should be a screenshot that show an expanded study with multiple modalities (CT, MRI) but not PET. -->
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The previous screenshot shows a study containing PET and CT images and both
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Basic Viewer and PET/CT Mode are available.
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## View Study
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The `Basic Viewer` mode is available for all studies by default. Click on the
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mode button to launch the viewer.
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---
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sidebar_position: 8
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---
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# Language
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OHIF supports internationalization capabilities and setting the general language
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of the Viewer.
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It should be noted that we don't have complete translations for all the components
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and all the languages; however, you can easily add the key value translation pairs
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following developer guides.
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Summary of language changing usage can be seen below:
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## Overview Video
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<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
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<iframe src="https://player.vimeo.com/video/843233906?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
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</div>
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{
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"label": "Basic Viewer",
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"position": 2
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}
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---
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sidebar_position: 7
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---
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# Hotkeys
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To open the hotkey assignment panel, you can click on the Preferences gear on the
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top right side of the viewer.
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Below, you can see the default hotkeys key bindings:
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Hotkeys can be assigned to custom bindings that persist for the duration of the browser session.
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---
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sidebar_position: 1
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sidebar_label: Overview
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---
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# Overview
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When you open a mode, viewport, toolbar and panels of the mode get shown.
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It is important to note that each mode has a different UI, which serves its purpose.
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Here we explain various components of `Basic Viewer` mode which includes measurement
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tracking functionalities.
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Basic viewer mode (longitudinal):
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Let's break different aspects of the viewer to the main components:
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- Left Panel (study panel): displays series thumbnails with series details
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- Viewport: renders the image and displays annotations
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- Right Panel (measurements): displays annotations details
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- Toolbar: displays tools and logo
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Now, we explain each component and its sub-elements in detail.
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---
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sidebar_position: 3
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---
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# Measurement Panel
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## Introduction
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In `Basic Viewer` mode, the right panel is the `Measurement Panel`. The Measurement Panel can be expanded or hidden by clicking on the arrow to the left of `Measurements`.
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<!-- We might want to make an entire section about the tracking workflow including SR hydration because it's pretty complicated. Let's review after the deploy branch is ready. Logic is in OHIF-63 OHIF-339 tickets for reference -->
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Select a measurement tool and mark an image to initiate measurement tracking. A pop-up will ask if you want to track measurements for the series on which the annotation was drawn.
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If you select `Yes`, the series becomes a `tracked series`, and the current drawn measurement and next measurements are shown on the measurement panel on the right.
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If you select `No`, the measurement becomes temporary. The next annotation made will repeat the measurement tracking prompt.
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If you select `No, do not ask again`, all annotations made on the study will be temporary.
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<!-- Temporary measurement screenshot -->
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## Labeling Measurements
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You can edit the measurement name by hovering over the measurement and selecting the edit icon. You can also label or relabel a measurement by right-clicking on it in the viewport.
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## Deleting a Measurement
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A measurement can be deleting by dragging it outside the image in the viewport or by right-clicking on the measurement in the viewport and selecting 'Delete'.
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## Jumping to a Measurement
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Measurement navigation inside the top viewport can be used to move to previous and next measurement.
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If a series containing a measurement is currently being displayed in a viewport, you can jump to display the measurement in the viewport by clicking on it in the Measurement Panel.
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## Export Measurements
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<!-- I think PDF and DICOM export didn't make it into this version but should be options. Let's confirm -->
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You can export the measurements by clicking on the `Export`. A CSV file will get downloaded to your local computer containing the drawn measurements.
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If you have set up your DICOM server to be able to store instances from the viewer, then you are able to create a report by clicking on the `Create Report`.
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This will create a DICOM Structured Report (SR) from the measurements and push it
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to the server.
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For instance, running the Viewer on a local DCM4CHEE:
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<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
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<iframe src="https://player.vimeo.com/video/843233857?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
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</div>
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## Overview Video
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An overview of measurement drawing and exporting can be seen below:
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<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
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<iframe src="https://player.vimeo.com/video/843233565?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
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</div>
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---
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sidebar_position: 4
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---
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# Measurement Tracking
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## Introduction
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OHIF-V3's `Basic Viewer` implements a `Measurement Tracking` workflow. Measurement
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tracking allows you to:
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- Draw annotations and have them shown in the measurement panel
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- Create a report from the tracked measurement and export them as DICOM SR
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- Use already exported DICOM SR to re-hydrate the measurements in the viewer
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## Status Icon
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Each viewport has a left icon indicating whether the series within the viewport
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contains:
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- tracked measurement OR
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- untracked measurement OR
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- Structured Report OR
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- Locked (uneditable) Structured Report
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In the following, we will discuss each category.
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### Tracked vs Untracked Measurements
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`OHIF-v3` implements a workflow for measurement tracking that can be seen below.
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In summary, when you create an annotation, a prompt will be shown whether to start tracking or not. If you start the tracking, the annotation style will change to a solid line, and annotation details get displayed on the measurement panel.
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On the other hand, if you decline the tracking prompt, the measurement will be considered "temporary," and annotation style remains as a dashed line and not shown on the right panel, and cannot be exported.
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Below, you can see different icons that appear for a tracked vs. untracked series in
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`OHIF-v3`.
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#### Overview video for starting the tracking for measurements:
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<!-- trackedMeasurements -->
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<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
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<iframe src="https://player.vimeo.com/video/843234022?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
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</div>
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<br></br>
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#### Overview video for not starting tracking for measurements:
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<!-- untrackedMeasurements -->
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<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
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<iframe src="https://player.vimeo.com/video/843234086?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
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</div>
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### Reading and Writing DICOM SR
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`OHIF-v3` provides full support for reading, writing and mapping the DICOM Structured
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Report (SR) to interactable `Cornerstone Tools`. When you load an already exported
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DICOM SR into the viewer, you will be prompted whether to track the measurements
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for the series or not.
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If you click Yes, DICOM SR measurements gets re-hydrated into the viewer and
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the series become a tracked series. However, If you say no and later decide to say track the measurements, you can always click on the SR button that will prompt you
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with the same message again.
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The full workflow for saving measurements to SR and loading SR into the viewer is shown below.
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#### Overview video for loading DICOM SR and making a tracked series:
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<!-- SR Restore and Yes -->
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<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
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<iframe src="https://player.vimeo.com/video/843233998?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
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</div>
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||||
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||||
<br></br>
|
||||
|
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#### Overview video for loading DICOM SR and not making a tracked series:
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<!-- SR Restore and No -->
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<!-- SR Export and measurement restore -->
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<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
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<iframe src="https://player.vimeo.com/video/843233976?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
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||||
</div>
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||||
|
||||
<br></br>
|
||||
|
||||
<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
|
||||
<iframe src="https://player.vimeo.com/video/843233958?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
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||||
</div>
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||||
|
||||
### Loading DICOM SR into an Already Tracked Series
|
||||
|
||||
If you have an already tracked series and try to load a DICOM SR measurements,
|
||||
you will be shown the following lock icon. This means that, you can review the
|
||||
DICOM SR measurement, manipulate image and draw "temporary" measurements; however,
|
||||
you cannot edit the DICOM SR measurement.
|
||||
|
||||
|
||||
|
||||
|
||||
<br></br>
|
||||
|
||||
|
||||
#### Overview video for loading DICOM SR inside an already tracked series:
|
||||
<!-- DICOMSRLockedTracked -->
|
||||
|
||||
|
||||
<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
|
||||
<iframe src="https://player.vimeo.com/video/843233929?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
|
||||
</div>
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||||
@@ -0,0 +1,32 @@
|
||||
---
|
||||
sidebar_position: 2
|
||||
---
|
||||
|
||||
# Study Panel
|
||||
|
||||
In `Basic Viewer` mode, the left panel includes Studies related to the current
|
||||
patient. You can see three main type of studies below
|
||||
|
||||
- Primary: The opened study from the study list. This study is always expanded
|
||||
by default.
|
||||
- Recent: All studies for the patient that contain study dates within 1 year of
|
||||
the primary study
|
||||
- All: All studies available for the patient contained within the source
|
||||
repository
|
||||
|
||||
The `Study Panel` displays the measurement tracking status of each series within
|
||||
a study. As you can see in the first picture, the dashed circle on the left side
|
||||
of each series demonstrates whether the series is being tracked for measurement
|
||||
or not.
|
||||
|
||||
<!-- We should resize this screenshot to make it smaller. We might want to add both screenshots in-line to make better use of horizontal space. Let's ask Dan -->
|
||||
|
||||
|
||||
|
||||
Studies can be expanded or collapsed by clicking on the study information in the
|
||||
Study Panel. If a series is being tracking within a study, the Measurement Panel
|
||||
will display this information while the study is collapsed.
|
||||
|
||||
<!-- We should link to refer to measurement tracking section -->
|
||||
|
||||
<!-- We need to add SR functionality descriptions to this section -->
|
||||
@@ -0,0 +1,85 @@
|
||||
---
|
||||
sidebar_position: 6
|
||||
---
|
||||
|
||||
|
||||
# Toolbar
|
||||
|
||||
The four main components of the toolbar are:
|
||||
|
||||
- Navigation back to the [Study List](../index.md)
|
||||
- Logo and white labelling
|
||||
- [Tools](#tools)
|
||||
- [Preferences](#preferences)
|
||||
|
||||
|
||||
|
||||
|
||||
## Tools
|
||||
This section displays all the available tools inside the mode.
|
||||
## Measurement tools
|
||||
The basic viewer comes with the following default measurement tools:
|
||||
|
||||
- Length Tool: Calculates the linear distance between two points in *mm*
|
||||
- Bidirectional Tool: Creates a measurement of the longest diameter (LD) and longest perpendicular diameter (LPD) in *mm*
|
||||
- Annotation: Used to create a qualitative marker with a freetext label
|
||||
- Ellipse: Measures an elliptical area in *mm<sup>2</sup>* and Hounsfield Units (HU)
|
||||
- Calibration Tool: Calibrate (or override) the Pixel Spacing Attribute (Physical distance in the patient between the center of each pixel, specified by a numeric pair - adjacent row spacing (delimiter) adjacent column spacing in mm)
|
||||
|
||||
When a measurement tool is selected from the toolbar, it becomes the `active` tool. Use the caret to expand the measurement tools and select another tool.
|
||||
<!-- We should add a smaller screenshot for each measurement tool. Maybe have a matrix with 4 identical sized screenshots in a box? Also we should make sure the screenshots have more realistic measurements -->
|
||||
|
||||
|
||||
|
||||
|
||||
## Window/Level
|
||||
The `Window/Level` tool enables manipulating the window level and window width of the rendered image. Click on the tool to enable freeform adjustment, then click and drag on the viewport to freely adjust the window/level.
|
||||
|
||||
Click on the caret to expand the tool and choose from predefined W/L settings for common imaging scenarios.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
## Pan and Zoom
|
||||
With the Zoom tool selected, click and drag the cursor on an image to adjust the zoom. The magnification level is displayed in the viewport.
|
||||
|
||||
With the Pan tool selected, click and drag the cursor on an image to adjust the image position.
|
||||
|
||||
## Image Capture
|
||||
Click on the Camera icon to download a high quality image capture using common image formats (png, jpg)
|
||||
|
||||
|
||||
|
||||
In the opened modal, the filename, image's width and height, and filetype and can be configured before downloading the image to your local computer.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
## Layout Selector
|
||||
Please see the `Viewport` section for details.
|
||||
|
||||
|
||||
## More Tools Menu
|
||||
- Reset View: Resets all image manipulation such as position, zoom, and W/L
|
||||
- Rotate Right: Flips the image 90 degrees clockwise
|
||||
- Flip Horizontally: Flips the image 180 degrees horizontally
|
||||
- Stack Scroll: Links all viewports containing images to scroll together
|
||||
- Magnify: Click on an image to magnify a particular area of interest
|
||||
- Invert: Inverts the color scale
|
||||
- Cine: Toggles the Cine player control in the currently selected viewport. Click the `x` on the Cine player or click the tool again to toggle off.
|
||||
- Angle: Measures an adjustable angle on an image
|
||||
- Probe: Drag the probe to see pixel values
|
||||
- Rectangle: Measures a rectangular area in mm^2 and HU
|
||||
|
||||
When a tool is selected from the `More Tools` menu, it becomes the active tool until it is replaced by clicking on a different tool in the More Tools menu or main toolbar.
|
||||
|
||||
<!-- Cine player tool -->
|
||||
## Overview Video
|
||||
An overview of tool usage can been seen below:
|
||||
|
||||
|
||||
<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
|
||||
<iframe src="https://player.vimeo.com/video/843233686?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
|
||||
</div>
|
||||
@@ -0,0 +1,39 @@
|
||||
---
|
||||
sidebar_position: 5
|
||||
---
|
||||
|
||||
# Viewport
|
||||
|
||||
Image visualization happens at the viewport which contains canvas or canvases that
|
||||
renders series.
|
||||
|
||||
|
||||
|
||||
|
||||
By default, you can modify:
|
||||
|
||||
- Zoom: right click dragging up or down
|
||||
- Contrast/brightness: left click dragging up/down to change contrast, and left/right for changing brightness
|
||||
- Pan: middle click dragging
|
||||
|
||||
|
||||
## Changing Series for display
|
||||
To change the displayed series, you can drag and drop the desired series from the left panel. Start, by dragging the thumbnail of the series, and drop it on the viewport.
|
||||
|
||||
## Changing Layout
|
||||
If you click on the layout icon on the toolbar, you can use the layout selector UI. After changing the layout, you can select studies for each new viewport by dragging and dropping in to the viewport.
|
||||
|
||||
After changing the layout from 1x1, you will see each viewport gets tagged by a letter,
|
||||
which matches its series section in the study list.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
## Overview Video
|
||||
An overview of viewport layout change, and manipulation can be seen below:
|
||||
|
||||
|
||||
<div style={{padding:"56.25% 0 0 0", position:"relative"}}>
|
||||
<iframe src="https://player.vimeo.com/video/843233651?badge=0&autopause=0&player_id=0&app_id=58479" frameBorder="0" allow="autoplay; fullscreen; picture-in-picture" allowFullScreen style= {{ position:"absolute",top:0,left:0,width:"100%",height:"100%"}} title="measurement-report"></iframe>
|
||||
</div>
|
||||
Reference in New Issue
Block a user