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* feat: Update to use pnpm (#6031) [simulated squash-merge] * feat: load DICOM SEG images via imageLoader * feat: load DICOM SEG images via imageLoader * PR review fixes * Test fragment of compressed multiframes * fix: Removed dependencies incorrectly * Update frame as a targetted change to avoid stripping remaining params * lock * Update test to agree with the missing representation branch * test(contour): contour color change coverage (#6042) * test(contour): contour interactions delete segment (#6069) --------- Co-authored-by: Bill Wallace <wayfarer3130@gmail.com> * chore(version): Update package versions to 3.13.0-beta.98 [skip ci] * feat(testing): OHIF Test Agent Skills (#5993) * chore(version): Update package versions to 3.13.0-beta.99 [skip ci] * test(contour): Add the ContourSegmentToggleLock.spec.ts test file to test contour locking (#6072) * chore(version): Update package versions to 3.13.0-beta.100 [skip ci] * chore(testing): Flock lock for playwright tests; Pin node version for OHIF; add more workers (#6099) * update Cypress apt deps for Ubuntu Noble (drop libgconf-2-4, libasound2→libasound2t64) * chore(version): Update package versions to 3.13.0-beta.101 [skip ci] * Debug fixes * perf(seg): pass explicit frame decode concurrency (16) to SEG loader Pass an explicit concurrency value (SEG_FRAME_DECODE_CONCURRENCY = 16) into createFromDicomSegImageId rather than relying on the adapter default, so the SEG frame fetch/decode parallelism is set at the call site and is ready to become configurable. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs(behaviours): add behaviours section + multiframe Part 10 prefetch proposal Start a "Behaviours" docs section for documenting how the system and UI behave end-to-end (observed behaviours, design proposals, and failure modes), with an index README and a Docusaurus category. First entry is the proposal for loading a multiframe SEG as a single Part 10 instance: prefetch the whole instance (gated by loadMultiframeAsPart10RaceTimeMs), parse it with dcmjs (handling multipart/related vs raw DICOM), and register the per-frame compressed pixels into the Cornerstone3D core image cache (the single uniform frame registry) so the per-frame load path is served locally while the standard decode path is unchanged. Best-effort: falls back to per-frame fetches on any failure. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Pre-cache the image data using a full part10 file for performance * Add customizations to specify type of segmentation save * Add clearcache of the cacheData * Bump @cornerstonejs/* pins 5.1.3 -> 5.4.10 to match libs/@cornerstonejs base libs/@cornerstonejs (fix/use-imageLoader-for-seg) is based on the released cs3d 5.4.10 (merge-base with origin/main is the 5.4.10 version bump), so pin OHIF to that release. The local branch changes still reach the app via the cs3d:link symlinks; these pins keep the lockfile/npm fallback aligned. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * Fix seg OOM * fix: file meta garbage element, bogus NumberOfFrames, unguarded source-map-loader - dicomWriter: drop the naturalized meta.TransferSyntaxUID assignment that dcmjs wrote as a garbage (0000,0000) element into every saved file's meta group (download / clipboard / local wadouri blob / local store); keep the hex 00020010 assignment, which is required for string-form _meta fallbacks. - registerNaturalizedDatasetForLocalWadouri: keep the computed frame count local so single-frame IODs (SR, RTSTRUCT) no longer gain a bogus NumberOfFrames element in their serialized form. - rsbuild.config: resolve source-map-loader opportunistically (it is not a project dependency; the rule only serves the gitignored cs3d-link workflow) so fresh clones no longer crash at config load. - Regression tests for both writer fixes (mutation-checked). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * PR review comment fixes * Update versions --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Co-authored-by: diattamo <mmddiatta@gmail.com> Co-authored-by: ohif-bot <danny.ri.brown+ohif-bot@gmail.com> Co-authored-by: Joe Boccanfuso <109477394+jbocce@users.noreply.github.com> |
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Total Metabolic Tumor Volume
Introduction
Total Metabolic Tumor Volume (TMTV) workflow mode enables quantitatively measurement of a tumor volume in a patient's body. This mode is accessible in any study that has a PT and CT image series as you can see below
Note: If the study does not have a PT and CT image series, the TMTV workflow mode will not be available and will become grayed out.
Layout
The designed layout for the viewports follows a predefined hanging protocol which will place 10 viewports containing CT, PT, Fusion and Maximum Intensity Projection (MIP) PT scenes.
The hanging protocol will match the CT and PT displaySets based on series description. In terms of PT displaySets, the hanging protocol will match the PT displaySet that has attenuated corrected PET image data.
As seen in the image below, the first row contains CT volume in 3 different views of Axial, Sagittal and Coronal. The second row contains PT volume in the same views as the first row. The last row contains the fusion volume and the viewport to the right is a MIP of the PT Volume in the Sagittal view.
Synchronization
The viewports in the 3 rows are synchronized both for the Camera and WindowLevel. It means that when you interact with the CT viewport (pan, zoom, scroll), the PT and Fusion viewports will be synchronized to the same view. In addition to camera synchronization, the window level of the CT viewport will be synchronized with the fusion viewport.
MIP
The tools that are activated on each viewport is unique to its data. For instance, the mouse scroll tool for PT, CT and Fusion viewports are scrolling through the image data (in different directions); however, the mouse scroll tool for the MIP viewport will rotate the camera to match the usecase for the MIP.
Panels
There are two panels that are available in the TMTV workflow mode and we will discuss them in detail below.
SUV Panel
This panel shows the PT metadata derived from the matched PT displaySet. The user can edit/change the metadata if needed, and by reloading the data the new metadata will be applied to the PT volume.
ROI Threshold Panel
The ROI Threshold panel is a panel that allows the user to use the RectangleROIStartEnd
tool from Cornerstone to define and edit a region of interest. Then, the user can
apply a threshold to the pixels in the ROI and save the result as a segmentation volume.
By applying each threshold to the ROI, the Total Metabolic Tumor Volume (TMTV), and the SUV Peak values will get calculated for the labelmap segments and shown in the panel.
Export Report
Finally, the results can be saved in the CSV format. The RectangleROI annotations can also be extracted as a dicom RT Structure Set and saved as a DICOM file.
Video Tutorial
Below you can see a video tutorial on how to use the TMTV workflow mode.
https://user-images.githubusercontent.com/7490180/171065443-35369fba-e955-48ac-94da-d262e0fccb6b.mp4