init

extensions/tmtv/.webpack/webpack.dev.js

@@ -0,0 +1,8 @@
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.base.js');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  return webpackCommon(env, argv, { SRC_DIR, DIST_DIR, ENTRY });
+};

extensions/tmtv/.webpack/webpack.prod.js

@@ -0,0 +1,54 @@
+const webpack = require('webpack');
+const { merge } = require('webpack-merge');
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.base.js');
+const pkg = require('./../package.json');
+
+const ROOT_DIR = path.join(__dirname, './..');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+const MiniCssExtractPlugin = require('mini-css-extract-plugin');
+
+const ENTRY = {
+  app: `${SRC_DIR}/index.tsx`,
+};
+
+const outputName = `ohif-${pkg.name.split('/').pop()}`;
+
+module.exports = (env, argv) => {
+  const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR, ENTRY });
+
+  return merge(commonConfig, {
+    stats: {
+      colors: true,
+      hash: true,
+      timings: true,
+      assets: true,
+      chunks: false,
+      chunkModules: false,
+      modules: false,
+      children: false,
+      warnings: true,
+    },
+    optimization: {
+      minimize: true,
+      sideEffects: false,
+    },
+    output: {
+      path: ROOT_DIR,
+      library: 'ohif-extension-tmtv',
+      libraryTarget: 'umd',
+      filename: pkg.main,
+    },
+    externals: [/\b(vtk.js)/, /\b(dcmjs)/, /\b(gl-matrix)/, /^@ohif/, /^@cornerstonejs/],
+    plugins: [
+      new webpack.optimize.LimitChunkCountPlugin({
+        maxChunks: 1,
+      }),
+      new MiniCssExtractPlugin({
+        filename: `./dist/${outputName}.css`,
+        chunkFilename: `./dist/${outputName}.css`,
+      }),
+    ],
+  });
+};

extensions/tmtv/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Open Health Imaging Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

extensions/tmtv/README.md

@@ -0,0 +1 @@
+# TMTV Extension

extensions/tmtv/babel.config.js

@@ -0,0 +1 @@
+module.exports = require('../../babel.config.js');

extensions/tmtv/package.json

@@ -0,0 +1,45 @@
+{
+  "name": "@ohif/extension-tmtv",
+  "version": "3.9.1",
+  "description": "OHIF extension for Total Metabolic Tumor Volume",
+  "author": "OHIF",
+  "license": "MIT",
+  "repository": "OHIF/Viewers",
+  "main": "dist/ohif-extension-tmtv.umd.js",
+  "module": "src/index.tsx",
+  "engines": {
+    "node": ">=14",
+    "npm": ">=6",
+    "yarn": ">=1.16.0"
+  },
+  "files": [
+    "dist",
+    "README.md"
+  ],
+  "publishConfig": {
+    "access": "public"
+  },
+  "scripts": {
+    "clean": "shx rm -rf dist",
+    "clean:deep": "yarn run clean && shx rm -rf node_modules",
+    "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --output-pathinfo",
+    "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js",
+    "build:package": "yarn run build",
+    "start": "yarn run dev",
+    "test:unit": "jest --watchAll",
+    "test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
+  },
+  "peerDependencies": {
+    "@ohif/core": "3.9.1",
+    "@ohif/ui": "3.9.1",
+    "dcmjs": "*",
+    "dicom-parser": "^1.8.9",
+    "hammerjs": "^2.0.8",
+    "prop-types": "^15.6.2",
+    "react": "^18.3.1"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.20.13",
+    "classnames": "^2.3.2"
+  }
+}

extensions/tmtv/src/Panels/PanelPetSUV.tsx

@@ -0,0 +1,246 @@
+import React, { useEffect, useState } from 'react';
+import PropTypes from 'prop-types';
+import { PanelSection, Input, Button } from '@ohif/ui';
+import { DicomMetadataStore } from '@ohif/core';
+import { useTranslation } from 'react-i18next';
+import { Separator } from '@ohif/ui-next';
+
+const DEFAULT_MEATADATA = {
+  PatientWeight: null,
+  PatientSex: null,
+  SeriesTime: null,
+  RadiopharmaceuticalInformationSequence: {
+    RadionuclideTotalDose: null,
+    RadionuclideHalfLife: null,
+    RadiopharmaceuticalStartTime: null,
+  },
+};
+
+/*
+ * PETSUV panel enables the user to modify the patient related information, such as
+ * patient sex, patientWeight. This is allowed since
+ * sometimes these metadata are missing or wrong. By changing them
+ * @param param0
+ * @returns
+ */
+export default function PanelPetSUV({ servicesManager, commandsManager }: withAppTypes) {
+  const { t } = useTranslation('PanelSUV');
+  const { displaySetService, toolGroupService, toolbarService, hangingProtocolService } =
+    servicesManager.services;
+  const [metadata, setMetadata] = useState(DEFAULT_MEATADATA);
+  const [ptDisplaySet, setPtDisplaySet] = useState(null);
+
+  const handleMetadataChange = metadata => {
+    setMetadata(prevState => {
+      const newState = { ...prevState };
+      Object.keys(metadata).forEach(key => {
+        if (typeof metadata[key] === 'object') {
+          newState[key] = {
+            ...prevState[key],
+            ...metadata[key],
+          };
+        } else {
+          newState[key] = metadata[key];
+        }
+      });
+      return newState;
+    });
+  };
+
+  const getMatchingPTDisplaySet = viewportMatchDetails => {
+    const ptDisplaySet = commandsManager.runCommand('getMatchingPTDisplaySet', {
+      viewportMatchDetails,
+    });
+
+    if (!ptDisplaySet) {
+      return;
+    }
+
+    const metadata = commandsManager.runCommand('getPTMetadata', {
+      ptDisplaySet,
+    });
+
+    return {
+      ptDisplaySet,
+      metadata,
+    };
+  };
+
+  useEffect(() => {
+    const displaySets = displaySetService.getActiveDisplaySets();
+    const { viewportMatchDetails } = hangingProtocolService.getMatchDetails();
+    if (!displaySets.length) {
+      return;
+    }
+
+    const displaySetInfo = getMatchingPTDisplaySet(viewportMatchDetails);
+
+    if (!displaySetInfo) {
+      return;
+    }
+
+    const { ptDisplaySet, metadata } = displaySetInfo;
+    setPtDisplaySet(ptDisplaySet);
+    setMetadata(metadata);
+  }, []);
+
+  // get the patientMetadata from the StudyInstanceUIDs and update the state
+  useEffect(() => {
+    const { unsubscribe } = hangingProtocolService.subscribe(
+      hangingProtocolService.EVENTS.PROTOCOL_CHANGED,
+      ({ viewportMatchDetails }) => {
+        const displaySetInfo = getMatchingPTDisplaySet(viewportMatchDetails);
+
+        if (!displaySetInfo) {
+          return;
+        }
+        const { ptDisplaySet, metadata } = displaySetInfo;
+        setPtDisplaySet(ptDisplaySet);
+        setMetadata(metadata);
+      }
+    );
+    return () => {
+      unsubscribe();
+    };
+  }, []);
+
+  function updateMetadata() {
+    if (!ptDisplaySet) {
+      throw new Error('No ptDisplaySet found');
+    }
+
+    // metadata should be dcmjs naturalized
+    DicomMetadataStore.updateMetadataForSeries(
+      ptDisplaySet.StudyInstanceUID,
+      ptDisplaySet.SeriesInstanceUID,
+      metadata
+    );
+
+    // update the displaySets
+    displaySetService.setDisplaySetMetadataInvalidated(ptDisplaySet.displaySetInstanceUID);
+
+    // Crosshair position depends on the metadata values such as the positioning interaction
+    // between series, so when the metadata is updated, the crosshairs need to be reset.
+    setTimeout(() => {
+      commandsManager.runCommand('resetCrosshairs');
+    }, 0);
+  }
+  return (
+    <>
+      <div className="ohif-scrollbar flex min-h-0 flex-auto select-none flex-col justify-between overflow-auto">
+        <div className="flex min-h-0 flex-1 flex-col bg-black text-[13px] font-[300]">
+          <PanelSection title={t('Patient Information')}>
+            <div className="flex flex-col">
+              <div className="bg-primary-dark flex flex-col gap-4 p-2">
+                <Input
+                  containerClassName={'!flex-row !justify-between items-center'}
+                  label={t('Patient Sex')}
+                  labelClassName="text-[13px] font-inter text-white"
+                  className="!m-0 !h-[26px] !w-[117px]"
+                  value={metadata.PatientSex || ''}
+                  onChange={e => {
+                    handleMetadataChange({
+                      PatientSex: e.target.value,
+                    });
+                  }}
+                />
+                <Input
+                  containerClassName={'!flex-row !justify-between items-center'}
+                  label={t('Weight')}
+                  labelChildren={<span className="text-aqua-pale"> kg</span>}
+                  labelClassName="text-[13px] font-inter text-white"
+                  className="!m-0 !h-[26px] !w-[117px]"
+                  value={metadata.PatientWeight || ''}
+                  onChange={e => {
+                    handleMetadataChange({
+                      PatientWeight: e.target.value,
+                    });
+                  }}
+                  id="weight-input"
+                />
+                <Input
+                  containerClassName={'!flex-row !justify-between items-center'}
+                  label={t('Total Dose')}
+                  labelChildren={<span className="text-aqua-pale"> bq</span>}
+                  labelClassName="text-[13px] font-inter text-white"
+                  className="!m-0 !h-[26px] !w-[117px]"
+                  value={
+                    metadata.RadiopharmaceuticalInformationSequence.RadionuclideTotalDose || ''
+                  }
+                  onChange={e => {
+                    handleMetadataChange({
+                      RadiopharmaceuticalInformationSequence: {
+                        RadionuclideTotalDose: e.target.value,
+                      },
+                    });
+                  }}
+                />
+                <Input
+                  containerClassName={'!flex-row !justify-between items-center'}
+                  label={t('Half Life')}
+                  labelChildren={<span className="text-aqua-pale"> s</span>}
+                  labelClassName="text-[13px] font-inter text-white"
+                  className="!m-0 !h-[26px] !w-[117px]"
+                  value={metadata.RadiopharmaceuticalInformationSequence.RadionuclideHalfLife || ''}
+                  onChange={e => {
+                    handleMetadataChange({
+                      RadiopharmaceuticalInformationSequence: {
+                        RadionuclideHalfLife: e.target.value,
+                      },
+                    });
+                  }}
+                />
+                <Input
+                  containerClassName={'!flex-row !justify-between items-center'}
+                  label={t('Injection Time')}
+                  labelChildren={<span className="text-aqua-pale"> s</span>}
+                  labelClassName="text-[13px] font-inter text-white"
+                  className="!m-0 !h-[26px] !w-[117px]"
+                  value={
+                    metadata.RadiopharmaceuticalInformationSequence.RadiopharmaceuticalStartTime ||
+                    ''
+                  }
+                  onChange={e => {
+                    handleMetadataChange({
+                      RadiopharmaceuticalInformationSequence: {
+                        RadiopharmaceuticalStartTime: e.target.value,
+                      },
+                    });
+                  }}
+                />
+                <Input
+                  containerClassName={'!flex-row !justify-between items-center'}
+                  label={t('Acquisition Time')}
+                  labelChildren={<span className="text-aqua-pale"> s</span>}
+                  labelClassName="text-[13px] font-inter text-white"
+                  className="!m-0 !h-[26px] !w-[117px]"
+                  value={metadata.SeriesTime || ''}
+                  onChange={() => {}}
+                />
+                <Button
+                  className="!h-[26px] !w-[115px] self-end !p-0"
+                  onClick={updateMetadata}
+                >
+                  Reload Data
+                </Button>
+              </div>
+            </div>
+          </PanelSection>
+        </div>
+      </div>
+    </>
+  );
+}
+
+PanelPetSUV.propTypes = {
+  servicesManager: PropTypes.shape({
+    services: PropTypes.shape({
+      measurementService: PropTypes.shape({
+        getMeasurements: PropTypes.func.isRequired,
+        subscribe: PropTypes.func.isRequired,
+        EVENTS: PropTypes.object.isRequired,
+        VALUE_TYPES: PropTypes.object.isRequired,
+      }).isRequired,
+    }).isRequired,
+  }).isRequired,
+};

extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/PanelROIThresholdExport.tsx

@@ -0,0 +1,76 @@
+import React, { useEffect } from 'react';
+import { useActiveViewportSegmentationRepresentations } from '@ohif/extension-cornerstone';
+import { handleROIThresholding } from '../../utils/handleROIThresholding';
+import { debounce } from '@ohif/core/src/utils';
+
+export default function PanelRoiThresholdSegmentation({
+  servicesManager,
+  commandsManager,
+}: withAppTypes) {
+  const { segmentationService } = servicesManager.services;
+  const { segmentationsWithRepresentations: segmentationsInfo } =
+    useActiveViewportSegmentationRepresentations({ servicesManager });
+
+  useEffect(() => {
+    const segmentationIds = segmentationsInfo.map(
+      segmentationInfo => segmentationInfo.segmentation.segmentationId
+    );
+
+    const initialRun = async () => {
+      for (const segmentationId of segmentationIds) {
+        await handleROIThresholding({
+          segmentationId,
+          commandsManager,
+          segmentationService,
+        });
+      }
+    };
+
+    initialRun();
+  }, []);
+
+  useEffect(() => {
+    const debouncedHandleROIThresholding = debounce(async eventDetail => {
+      const { segmentationId } = eventDetail;
+      await handleROIThresholding({
+        segmentationId,
+        commandsManager,
+        segmentationService,
+      });
+    }, 100);
+
+    const dataModifiedCallback = eventDetail => {
+      debouncedHandleROIThresholding(eventDetail);
+    };
+
+    const dataModifiedSubscription = segmentationService.subscribe(
+      segmentationService.EVENTS.SEGMENTATION_DATA_MODIFIED,
+      dataModifiedCallback
+    );
+
+    return () => {
+      dataModifiedSubscription.unsubscribe();
+    };
+  }, [commandsManager, segmentationService]);
+
+  // Find the first segmentation with a TMTV value since all of them have the same value
+  const tmtvSegmentation = segmentationsInfo.find(
+    info => info.segmentation.cachedStats?.tmtv !== undefined
+  );
+  const tmtvValue = tmtvSegmentation?.segmentation.cachedStats?.tmtv;
+
+  return (
+    <div className="mt-2 mb-10 flex flex-col">
+      <div className="invisible-scrollbar overflow-y-auto overflow-x-hidden">
+        {tmtvValue !== null && tmtvValue !== undefined ? (
+          <div className="bg-secondary-dark flex items-baseline justify-between px-2 py-1">
+            <span className="text-base font-bold uppercase tracking-widest text-white">
+              {'TMTV:'}
+            </span>
+            <div className="text-white">{`${tmtvValue.toFixed(3)} mL`}</div>
+          </div>
+        ) : null}
+      </div>
+    </div>
+  );
+}

extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/ROIThresholdConfiguration.tsx

@@ -0,0 +1,191 @@
+import React from 'react';
+import { Input, Label, Select, LegacyButton, LegacyButtonGroup } from '@ohif/ui';
+import { useTranslation } from 'react-i18next';
+
+export const ROI_STAT = 'roi_stat';
+const RANGE = 'range';
+
+const options = [
+  { value: ROI_STAT, label: 'Max', placeHolder: 'Max' },
+  { value: RANGE, label: 'Range', placeHolder: 'Range' },
+];
+
+function ROIThresholdConfiguration({ config, dispatch, runCommand }) {
+  const { t } = useTranslation('ROIThresholdConfiguration');
+
+  return (
+    <div className="bg-primary-dark flex flex-col space-y-4">
+      <div className="flex items-end space-x-2">
+        <div className="flex w-1/2 flex-col">
+          <Select
+            label={t('Strategy')}
+            closeMenuOnSelect={true}
+            className="border-primary-main mr-2 bg-black text-white "
+            options={options}
+            placeholder={options.find(option => option.value === config.strategy).placeHolder}
+            value={config.strategy}
+            onChange={({ value }) => {
+              dispatch({
+                type: 'setStrategy',
+                payload: {
+                  strategy: value,
+                },
+              });
+            }}
+          />
+        </div>
+        <div className="w-1/2">
+          {/* TODO Revisit design of LegacyButtonGroup later - for now use LegacyButton for its children.*/}
+          <LegacyButtonGroup>
+            <LegacyButton
+              size="initial"
+              className="px-2 py-2 text-base text-white"
+              color="primaryLight"
+              variant="outlined"
+              onClick={() => runCommand('setStartSliceForROIThresholdTool')}
+            >
+              {t('Start')}
+            </LegacyButton>
+            <LegacyButton
+              size="initial"
+              color="primaryLight"
+              variant="outlined"
+              className="px-2 py-2 text-base text-white"
+              onClick={() => runCommand('setEndSliceForROIThresholdTool')}
+            >
+              {t('End')}
+            </LegacyButton>
+          </LegacyButtonGroup>
+        </div>
+      </div>
+
+      {config.strategy === ROI_STAT && (
+        <Input
+          label={t('Percentage of Max SUV')}
+          labelClassName="text-[13px] font-inter text-white"
+          className="border-primary-main bg-black"
+          type="text"
+          containerClassName="mr-2"
+          value={config.weight}
+          onChange={e => {
+            dispatch({
+              type: 'setWeight',
+              payload: {
+                weight: e.target.value,
+              },
+            });
+          }}
+        />
+      )}
+      {config.strategy !== ROI_STAT && (
+        <div className="mr-2 text-sm">
+          <table>
+            <tbody>
+              <tr className="mt-2">
+                <td
+                  className="pr-4"
+                  colSpan="3"
+                >
+                  <Label
+                    className="font-inter text-[13px] text-white"
+                    text="Lower & Upper Ranges"
+                  ></Label>
+                </td>
+              </tr>
+              <tr className="mt-2">
+                <td className="pr-4 pt-2 text-center">
+                  <Label
+                    className="text-white"
+                    text="CT"
+                  ></Label>
+                </td>
+                <td>
+                  <div className="flex justify-between">
+                    <Input
+                      label={t('')}
+                      labelClassName="text-white"
+                      className="border-primary-main mt-2 bg-black"
+                      type="text"
+                      containerClassName="mr-2"
+                      value={config.ctLower}
+                      onChange={e => {
+                        dispatch({
+                          type: 'setThreshold',
+                          payload: {
+                            ctLower: e.target.value,
+                          },
+                        });
+                      }}
+                    />
+                    <Input
+                      label={t('')}
+                      labelClassName="text-white"
+                      className="border-primary-main mt-2 bg-black"
+                      type="text"
+                      containerClassName="mr-2"
+                      value={config.ctUpper}
+                      onChange={e => {
+                        dispatch({
+                          type: 'setThreshold',
+                          payload: {
+                            ctUpper: e.target.value,
+                          },
+                        });
+                      }}
+                    />
+                  </div>
+                </td>
+              </tr>
+              <tr>
+                <td className="pr-4 pt-2 text-center">
+                  <Label
+                    className="text-white"
+                    text="PT"
+                  ></Label>
+                </td>
+                <td>
+                  <div className="flex justify-between">
+                    <Input
+                      label={t('')}
+                      labelClassName="text-white"
+                      className="border-primary-main mt-2 bg-black"
+                      type="text"
+                      containerClassName="mr-2"
+                      value={config.ptLower}
+                      onChange={e => {
+                        dispatch({
+                          type: 'setThreshold',
+                          payload: {
+                            ptLower: e.target.value,
+                          },
+                        });
+                      }}
+                    />
+                    <Input
+                      label={t('')}
+                      labelClassName="text-white"
+                      className="border-primary-main mt-2 bg-black"
+                      type="text"
+                      containerClassName="mr-2"
+                      value={config.ptUpper}
+                      onChange={e => {
+                        dispatch({
+                          type: 'setThreshold',
+                          payload: {
+                            ptUpper: e.target.value,
+                          },
+                        });
+                      }}
+                    />
+                  </div>
+                </td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+      )}
+    </div>
+  );
+}
+
+export default ROIThresholdConfiguration;

extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/index.ts

@@ -0,0 +1,3 @@
+import PanelROIThresholdExport from './PanelROIThresholdExport';
+
+export default PanelROIThresholdExport;

extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/segmentationEditHandler.tsx

@@ -0,0 +1,63 @@
+import React from 'react';
+import { Input, Dialog, ButtonEnums } from '@ohif/ui';
+
+function segmentationItemEditHandler({ id, servicesManager }: withAppTypes) {
+  const { segmentationService, uiDialogService } = servicesManager.services;
+
+  const segmentation = segmentationService.getSegmentation(id);
+
+  const onSubmitHandler = ({ action, value }) => {
+    switch (action.id) {
+      case 'save': {
+        segmentationService.addOrUpdateSegmentation({
+          ...segmentation,
+          ...value,
+        });
+      }
+    }
+    uiDialogService.dismiss({ id: 'enter-annotation' });
+  };
+
+  uiDialogService.create({
+    id: 'enter-annotation',
+    centralize: true,
+    isDraggable: false,
+    showOverlay: true,
+    content: Dialog,
+    contentProps: {
+      title: 'Enter your Segmentation',
+      noCloseButton: true,
+      value: { label: segmentation.label || '' },
+      body: ({ value, setValue }) => {
+        const onChangeHandler = event => {
+          event.persist();
+          setValue(value => ({ ...value, label: event.target.value }));
+        };
+
+        const onKeyPressHandler = event => {
+          if (event.key === 'Enter') {
+            onSubmitHandler({ value, action: { id: 'save' } });
+          }
+        };
+        return (
+          <Input
+            autoFocus
+            className="border-primary-main bg-black"
+            type="text"
+            containerClassName="mr-2"
+            value={value.label}
+            onChange={onChangeHandler}
+            onKeyPress={onKeyPressHandler}
+          />
+        );
+      },
+      actions: [
+        { id: 'cancel', text: 'Cancel', type: ButtonEnums.type.secondary },
+        { id: 'save', text: 'Save', type: ButtonEnums.type.primary },
+      ],
+      onSubmit: onSubmitHandler,
+    },
+  });
+}
+
+export default segmentationItemEditHandler;

extensions/tmtv/src/Panels/PanelTMTV.tsx

@@ -0,0 +1,62 @@
+import React from 'react';
+import {
+  PanelSegmentation,
+  useActiveViewportSegmentationRepresentations,
+} from '@ohif/extension-cornerstone';
+import { Button, Icons } from '@ohif/ui-next';
+
+export default function PanelTMTV({
+  servicesManager,
+  commandsManager,
+  extensionManager,
+  configuration,
+}: withAppTypes) {
+  return (
+    <>
+      <PanelSegmentation
+        servicesManager={servicesManager}
+        commandsManager={commandsManager}
+        extensionManager={extensionManager}
+        configuration={configuration}
+      >
+        <ExportCSV
+          servicesManager={servicesManager}
+          commandsManager={commandsManager}
+        />
+      </PanelSegmentation>
+    </>
+  );
+}
+
+const ExportCSV = ({ servicesManager, commandsManager }: withAppTypes) => {
+  const { segmentationsWithRepresentations: representations } =
+    useActiveViewportSegmentationRepresentations({ servicesManager });
+
+  const tmtv = representations[0]?.segmentation.cachedStats?.tmtv;
+
+  const segmentations = representations.map(representation => representation.segmentation);
+
+  if (!segmentations.length) {
+    return null;
+  }
+
+  return (
+    <div className="flex h-8 w-full items-center rounded pr-0.5">
+      <Button
+        size="sm"
+        variant="ghost"
+        className="pl-1.5"
+        onClick={() => {
+          commandsManager.runCommand('exportTMTVReportCSV', {
+            segmentations,
+            tmtv,
+            config: {},
+          });
+        }}
+      >
+        <Icons.Download />
+        <span className="pl-1">CSV</span>
+      </Button>
+    </div>
+  );
+};

extensions/tmtv/src/Panels/RectangleROIOptions.tsx

@@ -0,0 +1,136 @@
+import React, { useState, useCallback, useReducer, useEffect } from 'react';
+import { Button } from '@ohif/ui';
+import ROIThresholdConfiguration, {
+  ROI_STAT,
+} from './PanelROIThresholdSegmentation/ROIThresholdConfiguration';
+import * as cs3dTools from '@cornerstonejs/tools';
+
+const LOWER_CT_THRESHOLD_DEFAULT = -1024;
+const UPPER_CT_THRESHOLD_DEFAULT = 1024;
+const LOWER_PT_THRESHOLD_DEFAULT = 2.5;
+const UPPER_PT_THRESHOLD_DEFAULT = 100;
+const WEIGHT_DEFAULT = 0.41; // a default weight for suv max often used in the literature
+const DEFAULT_STRATEGY = ROI_STAT;
+
+function reducer(state, action) {
+  const { payload } = action;
+  const { strategy, ctLower, ctUpper, ptLower, ptUpper, weight } = payload;
+
+  switch (action.type) {
+    case 'setStrategy':
+      return {
+        ...state,
+        strategy,
+      };
+    case 'setThreshold':
+      return {
+        ...state,
+        ctLower: ctLower ? ctLower : state.ctLower,
+        ctUpper: ctUpper ? ctUpper : state.ctUpper,
+        ptLower: ptLower ? ptLower : state.ptLower,
+        ptUpper: ptUpper ? ptUpper : state.ptUpper,
+      };
+    case 'setWeight':
+      return {
+        ...state,
+        weight,
+      };
+    default:
+      return state;
+  }
+}
+
+function RectangleROIOptions({ servicesManager, commandsManager }: withAppTypes) {
+  const { segmentationService } = servicesManager.services;
+  const [selectedSegmentationId, setSelectedSegmentationId] = useState(null);
+
+  const runCommand = useCallback(
+    (commandName, commandOptions = {}) => {
+      return commandsManager.runCommand(commandName, commandOptions);
+    },
+    [commandsManager]
+  );
+
+  const [config, dispatch] = useReducer(reducer, {
+    strategy: DEFAULT_STRATEGY,
+    ctLower: LOWER_CT_THRESHOLD_DEFAULT,
+    ctUpper: UPPER_CT_THRESHOLD_DEFAULT,
+    ptLower: LOWER_PT_THRESHOLD_DEFAULT,
+    ptUpper: UPPER_PT_THRESHOLD_DEFAULT,
+    weight: WEIGHT_DEFAULT,
+  });
+
+  const handleROIThresholding = useCallback(() => {
+    const segmentationId = selectedSegmentationId;
+    const activeSegmentIndex =
+      cs3dTools.segmentation.segmentIndex.getActiveSegmentIndex(segmentationId);
+
+    // run the threshold based on the active segment index
+    // Todo: later find a way to associate each rectangle with a segment (e.g., maybe with color?)
+    runCommand('thresholdSegmentationByRectangleROITool', {
+      segmentationId,
+      config,
+      segmentIndex: activeSegmentIndex,
+    });
+  }, [selectedSegmentationId, config]);
+
+  useEffect(() => {
+    const segmentations = segmentationService.getSegmentationRepresentations();
+
+    if (!segmentations.length) {
+      return;
+    }
+
+    const isActive = segmentations.find(seg => seg.isActive);
+    setSelectedSegmentationId(isActive.id);
+  }, []);
+
+  /**
+   * Update UI based on segmentation changes (added, removed, updated)
+   */
+  useEffect(() => {
+    // ~~ Subscription
+    const updated = segmentationService.EVENTS.SEGMENTATION_MODIFIED;
+    const subscriptions = [];
+
+    [updated].forEach(evt => {
+      const { unsubscribe } = segmentationService.subscribe(evt, () => {
+        const segmentations = segmentationService.getSegmentationRepresentations();
+
+        if (!segmentations.length) {
+          return;
+        }
+
+        const isActive = segmentations.find(seg => seg.isActive);
+        setSelectedSegmentationId(isActive.id);
+      });
+      subscriptions.push(unsubscribe);
+    });
+
+    return () => {
+      subscriptions.forEach(unsub => {
+        unsub();
+      });
+    };
+  }, []);
+
+  return (
+    <div className="invisible-scrollbar mb-2 flex flex-col overflow-y-auto overflow-x-hidden">
+      <ROIThresholdConfiguration
+        config={config}
+        dispatch={dispatch}
+        runCommand={runCommand}
+      />
+      {selectedSegmentationId !== null && (
+        <Button
+          className="mt-2 !h-[26px] !w-[75px]"
+          onClick={handleROIThresholding}
+        >
+          Run
+        </Button>
+      )}
+    </div>
+  );
+}
+
+export default RectangleROIOptions;

extensions/tmtv/src/Panels/index.tsx

@@ -0,0 +1,4 @@
+import PanelPetSUV from './PanelPetSUV';
+import PanelROIThresholdExport from './PanelROIThresholdSegmentation';
+
+export { PanelPetSUV, PanelROIThresholdExport };

extensions/tmtv/src/commandsModule.ts

@@ -0,0 +1,703 @@
+import OHIF from '@ohif/core';
+import * as cs from '@cornerstonejs/core';
+import * as csTools from '@cornerstonejs/tools';
+import { classes } from '@ohif/core';
+import getThresholdValues from './utils/getThresholdValue';
+import createAndDownloadTMTVReport from './utils/createAndDownloadTMTVReport';
+
+import dicomRTAnnotationExport from './utils/dicomRTAnnotationExport/RTStructureSet';
+
+import { getWebWorkerManager } from '@cornerstonejs/core';
+import { Enums } from '@cornerstonejs/tools';
+
+const { SegmentationRepresentations } = Enums;
+
+const metadataProvider = classes.MetadataProvider;
+const ROI_THRESHOLD_MANUAL_TOOL_IDS = [
+  'RectangleROIStartEndThreshold',
+  'RectangleROIThreshold',
+  'CircleROIStartEndThreshold',
+];
+
+const workerManager = getWebWorkerManager();
+
+const options = {
+  maxWorkerInstances: 1,
+  autoTerminateOnIdle: {
+    enabled: true,
+    idleTimeThreshold: 3000,
+  },
+};
+
+// Register the task
+const workerFn = () => {
+  return new Worker(new URL('./utils/calculateSUVPeakWorker.js', import.meta.url), {
+    name: 'suv-peak-worker', // name used by the browser to name the worker
+  });
+};
+
+function getVolumesFromSegmentation(segmentationId) {
+  const csSegmentation = csTools.segmentation.state.getSegmentation(segmentationId);
+  const labelmapData = csSegmentation.representationData[
+    SegmentationRepresentations.Labelmap
+  ] as csTools.Types.LabelmapToolOperationDataVolume;
+
+  const { volumeId, referencedVolumeId } = labelmapData;
+  const labelmapVolume = cs.cache.getVolume(volumeId);
+  const referencedVolume = cs.cache.getVolume(referencedVolumeId);
+
+  return { labelmapVolume, referencedVolume };
+}
+
+function getLabelmapVolumeFromSegmentation(segmentation) {
+  const { representationData } = segmentation;
+  const { volumeId } = representationData[
+    SegmentationRepresentations.Labelmap
+  ] as csTools.Types.LabelmapToolOperationDataVolume;
+
+  return cs.cache.getVolume(volumeId);
+}
+
+const commandsModule = ({ servicesManager, commandsManager, extensionManager }: withAppTypes) => {
+  const {
+    viewportGridService,
+    uiNotificationService,
+    displaySetService,
+    hangingProtocolService,
+    toolGroupService,
+    cornerstoneViewportService,
+    segmentationService,
+  } = servicesManager.services;
+
+  const utilityModule = extensionManager.getModuleEntry(
+    '@ohif/extension-cornerstone.utilityModule.common'
+  );
+
+  const { getEnabledElement } = utilityModule.exports;
+
+  function _getActiveViewportsEnabledElement() {
+    const { activeViewportId } = viewportGridService.getState();
+    const { element } = getEnabledElement(activeViewportId) || {};
+    const enabledElement = cs.getEnabledElement(element);
+    return enabledElement;
+  }
+
+  function _getAnnotationsSelectedByToolNames(toolNames) {
+    return toolNames.reduce((allAnnotationUIDs, toolName) => {
+      const annotationUIDs =
+        csTools.annotation.selection.getAnnotationsSelectedByToolName(toolName);
+
+      return allAnnotationUIDs.concat(annotationUIDs);
+    }, []);
+  }
+
+  const actions = {
+    getMatchingPTDisplaySet: ({ viewportMatchDetails }) => {
+      // Todo: this is assuming that the hanging protocol has successfully matched
+      // the correct PT. For future, we should have a way to filter out the PTs
+      // that are in the viewer layout (but then we have the problem of the attenuation
+      // corrected PT vs the non-attenuation correct PT)
+
+      let ptDisplaySet = null;
+      for (const [viewportId, viewportDetails] of viewportMatchDetails) {
+        const { displaySetsInfo } = viewportDetails;
+        const displaySets = displaySetsInfo.map(({ displaySetInstanceUID }) =>
+          displaySetService.getDisplaySetByUID(displaySetInstanceUID)
+        );
+
+        if (!displaySets || displaySets.length === 0) {
+          continue;
+        }
+
+        ptDisplaySet = displaySets.find(displaySet => displaySet.Modality === 'PT');
+        if (ptDisplaySet) {
+          break;
+        }
+      }
+
+      return ptDisplaySet;
+    },
+    getPTMetadata: ({ ptDisplaySet }) => {
+      const dataSource = extensionManager.getDataSources()[0];
+      const imageIds = dataSource.getImageIdsForDisplaySet(ptDisplaySet);
+
+      const firstImageId = imageIds[0];
+      const instance = metadataProvider.get('instance', firstImageId);
+      if (instance.Modality !== 'PT') {
+        return;
+      }
+
+      const metadata = {
+        SeriesTime: instance.SeriesTime,
+        Modality: instance.Modality,
+        PatientSex: instance.PatientSex,
+        PatientWeight: instance.PatientWeight,
+        RadiopharmaceuticalInformationSequence: {
+          RadionuclideTotalDose:
+            instance.RadiopharmaceuticalInformationSequence[0].RadionuclideTotalDose,
+          RadionuclideHalfLife:
+            instance.RadiopharmaceuticalInformationSequence[0].RadionuclideHalfLife,
+          RadiopharmaceuticalStartTime:
+            instance.RadiopharmaceuticalInformationSequence[0].RadiopharmaceuticalStartTime,
+          RadiopharmaceuticalStartDateTime:
+            instance.RadiopharmaceuticalInformationSequence[0].RadiopharmaceuticalStartDateTime,
+        },
+      };
+
+      return metadata;
+    },
+    createNewLabelmapFromPT: async ({ label }) => {
+      // Create a segmentation of the same resolution as the source data
+      // using volumeLoader.createAndCacheDerivedVolume.
+
+      const { viewportMatchDetails } = hangingProtocolService.getMatchDetails();
+
+      const ptDisplaySet = actions.getMatchingPTDisplaySet({
+        viewportMatchDetails,
+      });
+
+      let withPTViewportId = null;
+
+      for (const [viewportId, { displaySetsInfo }] of viewportMatchDetails.entries()) {
+        const isPT = displaySetsInfo.some(
+          ({ displaySetInstanceUID }) =>
+            displaySetInstanceUID === ptDisplaySet.displaySetInstanceUID
+        );
+
+        if (isPT) {
+          withPTViewportId = viewportId;
+          break;
+        }
+      }
+
+      if (!ptDisplaySet) {
+        uiNotificationService.error('No matching PT display set found');
+        return;
+      }
+
+      const currentSegmentations =
+        segmentationService.getSegmentationRepresentations(withPTViewportId);
+
+      const displaySet = displaySetService.getDisplaySetByUID(ptDisplaySet.displaySetInstanceUID);
+
+      const segmentationId = await segmentationService.createLabelmapForDisplaySet(displaySet, {
+        label: `Segmentation ${currentSegmentations.length + 1}`,
+        segments: { 1: { label: 'Segment 1', active: true } },
+      });
+
+      segmentationService.addSegmentationRepresentation(withPTViewportId, {
+        segmentationId,
+      });
+
+      return segmentationId;
+    },
+    thresholdSegmentationByRectangleROITool: ({ segmentationId, config, segmentIndex }) => {
+      const segmentation = csTools.segmentation.state.getSegmentation(segmentationId);
+
+      const { representationData } = segmentation;
+      const { displaySetMatchDetails: matchDetails } = hangingProtocolService.getMatchDetails();
+      const volumeLoaderScheme = 'cornerstoneStreamingImageVolume'; // Loader id which defines which volume loader to use
+
+      const ctDisplaySet = matchDetails.get('ctDisplaySet');
+      const ctVolumeId = `${volumeLoaderScheme}:${ctDisplaySet.displaySetInstanceUID}`; // VolumeId with loader id + volume id
+
+      const { volumeId: segVolumeId } = representationData[
+        SegmentationRepresentations.Labelmap
+      ] as csTools.Types.LabelmapToolOperationDataVolume;
+      const { referencedVolumeId } = cs.cache.getVolume(segVolumeId);
+
+      const annotationUIDs = _getAnnotationsSelectedByToolNames(ROI_THRESHOLD_MANUAL_TOOL_IDS);
+
+      if (annotationUIDs.length === 0) {
+        uiNotificationService.show({
+          title: 'Commands Module',
+          message: 'No ROIThreshold Tool is Selected',
+          type: 'error',
+        });
+        return;
+      }
+
+      const labelmapVolume = cs.cache.getVolume(segmentationId);
+      let referencedVolume = cs.cache.getVolume(referencedVolumeId);
+      const ctReferencedVolume = cs.cache.getVolume(ctVolumeId);
+
+      // check if viewport is
+
+      if (!referencedVolume) {
+        throw new Error('No Reference volume found');
+      }
+
+      if (!labelmapVolume) {
+        throw new Error('No Reference labelmap found');
+      }
+
+      const annotation = csTools.annotation.state.getAnnotation(annotationUIDs[0]);
+
+      const {
+        metadata: {
+          enabledElement: { viewport },
+        },
+      } = annotation;
+
+      const showingReferenceVolume = viewport.hasVolumeId(referencedVolumeId);
+
+      if (!showingReferenceVolume) {
+        // if the reference volume is not being displayed, we can't
+        // rely on it for thresholding, we have couple of options here
+        // 1. We choose whatever volume is being displayed
+        // 2. We check if it is a fusion viewport, we pick the volume
+        // that matches the size and dimensions of the labelmap. This might
+        // happen if the 4D PT is converted to a computed volume and displayed
+        // and wants to threshold the labelmap
+        // 3. We throw an error
+        const displaySetInstanceUIDs = viewportGridService.getDisplaySetsUIDsForViewport(
+          viewport.id
+        );
+
+        displaySetInstanceUIDs.forEach(displaySetInstanceUID => {
+          const volume = cs.cache
+            .getVolumes()
+            .find(volume => volume.volumeId.includes(displaySetInstanceUID));
+
+          if (
+            cs.utilities.isEqual(volume.dimensions, labelmapVolume.dimensions) &&
+            cs.utilities.isEqual(volume.spacing, labelmapVolume.spacing)
+          ) {
+            referencedVolume = volume;
+          }
+        });
+      }
+
+      const { ptLower, ptUpper, ctLower, ctUpper } = getThresholdValues(
+        annotationUIDs,
+        [referencedVolume, ctReferencedVolume],
+        config
+      );
+
+      return csTools.utilities.segmentation.rectangleROIThresholdVolumeByRange(
+        annotationUIDs,
+        labelmapVolume,
+        [
+          { volume: referencedVolume, lower: ptLower, upper: ptUpper },
+          { volume: ctReferencedVolume, lower: ctLower, upper: ctUpper },
+        ],
+        { overwrite: true, segmentIndex }
+      );
+    },
+    calculateSuvPeak: async ({ segmentationId, segmentIndex }) => {
+      const segmentation = segmentationService.getSegmentation(segmentationId);
+
+      const { representationData } = segmentation;
+      const { volumeId, referencedVolumeId } = representationData[
+        SegmentationRepresentations.Labelmap
+      ] as csTools.Types.LabelmapToolOperationDataVolume;
+
+      const labelmap = cs.cache.getVolume(volumeId);
+      const referencedVolume = cs.cache.getVolume(referencedVolumeId);
+
+      // if we put it in the top, it will appear in other modes
+      workerManager.registerWorker('suv-peak-worker', workerFn, options);
+
+      const annotationUIDs = _getAnnotationsSelectedByToolNames(ROI_THRESHOLD_MANUAL_TOOL_IDS);
+
+      const annotations = annotationUIDs.map(annotationUID =>
+        csTools.annotation.state.getAnnotation(annotationUID)
+      );
+
+      const labelmapProps = {
+        dimensions: labelmap.dimensions,
+        origin: labelmap.origin,
+        direction: labelmap.direction,
+        spacing: labelmap.spacing,
+        metadata: labelmap.metadata,
+        scalarData: labelmap.voxelManager.getCompleteScalarDataArray(),
+      };
+
+      const referenceVolumeProps = {
+        dimensions: referencedVolume.dimensions,
+        origin: referencedVolume.origin,
+        direction: referencedVolume.direction,
+        spacing: referencedVolume.spacing,
+        metadata: referencedVolume.metadata,
+        scalarData: referencedVolume.voxelManager.getCompleteScalarDataArray(),
+      };
+
+      // metadata in annotations has enabledElement which is not serializable
+      // we need to remove it
+      // Todo: we should probably have a sanitization function for this
+      const annotationsToSend = annotations.map(annotation => {
+        return {
+          ...annotation,
+          metadata: {
+            ...annotation.metadata,
+            enabledElement: {
+              ...annotation.metadata.enabledElement,
+              viewport: null,
+              renderingEngine: null,
+              element: null,
+            },
+          },
+        };
+      });
+
+      const suvPeak =
+        (await workerManager.executeTask('suv-peak-worker', 'calculateSuvPeak', {
+          labelmapProps,
+          referenceVolumeProps,
+          annotations: annotationsToSend,
+          segmentIndex,
+        })) || {};
+
+      return {
+        suvPeak: suvPeak.mean,
+        suvMax: suvPeak.max,
+        suvMaxIJK: suvPeak.maxIJK,
+        suvMaxLPS: suvPeak.maxLPS,
+      };
+    },
+    getLesionStats: ({ segmentationId, segmentIndex = 1 }) => {
+      const { labelmapVolume, referencedVolume } = getVolumesFromSegmentation(segmentationId);
+      const { voxelManager: segVoxelManager, imageData, spacing } = labelmapVolume;
+      const { voxelManager: refVoxelManager } = referencedVolume;
+
+      let segmentationMax = -Infinity;
+      let segmentationMin = Infinity;
+      const segmentationValues = [];
+      let voxelCount = 0;
+
+      const callback = ({ value, index }) => {
+        if (value === segmentIndex) {
+          const refValue = refVoxelManager.getAtIndex(index) as number;
+          segmentationValues.push(refValue);
+          if (refValue > segmentationMax) {
+            segmentationMax = refValue;
+          }
+          if (refValue < segmentationMin) {
+            segmentationMin = refValue;
+          }
+          voxelCount++;
+        }
+      };
+
+      segVoxelManager.forEach(callback, { imageData });
+      const mean = segmentationValues.reduce((a, b) => a + b, 0) / voxelCount;
+      const stats = {
+        minValue: segmentationMin,
+        maxValue: segmentationMax,
+        meanValue: mean,
+        stdValue: Math.sqrt(
+          segmentationValues.map(k => (k - mean) ** 2).reduce((acc, curr) => acc + curr, 0) /
+            voxelCount
+        ),
+        volume: voxelCount * spacing[0] * spacing[1] * spacing[2] * 1e-3,
+      };
+
+      return stats;
+    },
+    calculateLesionGlycolysis: ({ lesionStats }) => {
+      const { meanValue, volume } = lesionStats;
+
+      return {
+        lesionGlyoclysisStats: volume * meanValue,
+      };
+    },
+    calculateTMTV: async ({ segmentations }) => {
+      const labelmapProps = segmentations.map(segmentation => {
+        const labelmap = getLabelmapVolumeFromSegmentation(segmentation);
+        return {
+          dimensions: labelmap.dimensions,
+          spacing: labelmap.spacing,
+          scalarData: labelmap.voxelManager.getCompleteScalarDataArray(),
+          origin: labelmap.origin,
+          direction: labelmap.direction,
+        };
+      });
+
+      if (!labelmapProps.length) {
+        return;
+      }
+
+      return await workerManager.executeTask('suv-peak-worker', 'calculateTMTV', labelmapProps);
+    },
+    exportTMTVReportCSV: async ({ segmentations, tmtv, config, options }) => {
+      const segReport = commandsManager.runCommand('getSegmentationCSVReport', {
+        segmentations,
+      });
+
+      const tlg = await actions.getTotalLesionGlycolysis({ segmentations });
+      const additionalReportRows = [
+        { key: 'Total Lesion Glycolysis', value: { tlg: tlg.toFixed(4) } },
+        { key: 'Threshold Configuration', value: { ...config } },
+      ];
+
+      if (tmtv !== undefined) {
+        additionalReportRows.unshift({
+          key: 'Total Metabolic Tumor Volume',
+          value: { tmtv },
+        });
+      }
+
+      createAndDownloadTMTVReport(segReport, additionalReportRows, options);
+    },
+    getTotalLesionGlycolysis: async ({ segmentations }) => {
+      const labelmapProps = segmentations.map(segmentation => {
+        const labelmap = getLabelmapVolumeFromSegmentation(segmentation);
+        return {
+          dimensions: labelmap.dimensions,
+          spacing: labelmap.spacing,
+          scalarData: labelmap.voxelManager.getCompleteScalarDataArray(),
+          origin: labelmap.origin,
+          direction: labelmap.direction,
+        };
+      });
+
+      const { referencedVolume: ptVolume } = getVolumesFromSegmentation(
+        segmentations[0].segmentationId
+      );
+
+      const ptVolumeProps = {
+        dimensions: ptVolume.dimensions,
+        spacing: ptVolume.spacing,
+        scalarData: ptVolume.voxelManager.getCompleteScalarDataArray(),
+        origin: ptVolume.origin,
+        direction: ptVolume.direction,
+      };
+
+      return await workerManager.executeTask('suv-peak-worker', 'getTotalLesionGlycolysis', {
+        labelmapProps,
+        referenceVolumeProps: ptVolumeProps,
+      });
+    },
+    setStartSliceForROIThresholdTool: () => {
+      const { viewport } = _getActiveViewportsEnabledElement();
+      const { focalPoint } = viewport.getCamera();
+
+      const selectedAnnotationUIDs = _getAnnotationsSelectedByToolNames(
+        ROI_THRESHOLD_MANUAL_TOOL_IDS
+      );
+
+      const annotationUID = selectedAnnotationUIDs[0];
+
+      const annotation = csTools.annotation.state.getAnnotation(annotationUID);
+
+      // set the current focal point
+      annotation.data.startCoordinate = focalPoint;
+      // IMPORTANT: invalidate the toolData for the cached stat to get updated
+      // and re-calculate the projection points
+      annotation.invalidated = true;
+      viewport.render();
+    },
+    setEndSliceForROIThresholdTool: () => {
+      const { viewport } = _getActiveViewportsEnabledElement();
+
+      const selectedAnnotationUIDs = _getAnnotationsSelectedByToolNames(
+        ROI_THRESHOLD_MANUAL_TOOL_IDS
+      );
+
+      const annotationUID = selectedAnnotationUIDs[0];
+
+      const annotation = csTools.annotation.state.getAnnotation(annotationUID);
+
+      // get the current focal point
+      const focalPointToEnd = viewport.getCamera().focalPoint;
+      annotation.data.endCoordinate = focalPointToEnd;
+
+      // IMPORTANT: invalidate the toolData for the cached stat to get updated
+      // and re-calculate the projection points
+      annotation.invalidated = true;
+
+      viewport.render();
+    },
+    createTMTVRTReport: () => {
+      // get all Rectangle ROI annotation
+      const stateManager = csTools.annotation.state.getAnnotationManager();
+
+      const annotations = [];
+
+      Object.keys(stateManager.annotations).forEach(frameOfReferenceUID => {
+        const forAnnotations = stateManager.annotations[frameOfReferenceUID];
+        const ROIAnnotations = ROI_THRESHOLD_MANUAL_TOOL_IDS.reduce(
+          (annotations, toolName) => [...annotations, ...(forAnnotations[toolName] ?? [])],
+          []
+        );
+
+        annotations.push(...ROIAnnotations);
+      });
+
+      commandsManager.runCommand('exportRTReportForAnnotations', {
+        annotations,
+      });
+    },
+    getSegmentationCSVReport: ({ segmentations }) => {
+      if (!segmentations || !segmentations.length) {
+        segmentations = segmentationService.getSegmentations();
+      }
+
+      const report = {};
+
+      for (const segmentation of segmentations) {
+        const { label, segmentationId, representationData } =
+          segmentation as csTools.Types.Segmentation;
+        const id = segmentationId;
+
+        const segReport = { id, label };
+
+        if (!representationData) {
+          report[id] = segReport;
+          continue;
+        }
+
+        const { cachedStats } = segmentation.segments[1] || {}; // Assuming we want stats from the first segment
+
+        if (cachedStats) {
+          Object.entries(cachedStats).forEach(([key, value]) => {
+            if (typeof value !== 'object') {
+              segReport[key] = value;
+            } else {
+              Object.entries(value).forEach(([subKey, subValue]) => {
+                const newKey = `${key}_${subKey}`;
+                segReport[newKey] = subValue;
+              });
+            }
+          });
+        }
+
+        const labelmapVolume =
+          segmentation.representationData[SegmentationRepresentations.Labelmap];
+
+        if (!labelmapVolume) {
+          report[id] = segReport;
+          continue;
+        }
+
+        const referencedVolumeId = labelmapVolume.referencedVolumeId;
+
+        const referencedVolume = cs.cache.getVolume(referencedVolumeId);
+
+        if (!referencedVolume) {
+          report[id] = segReport;
+          continue;
+        }
+
+        if (!referencedVolume.imageIds || !referencedVolume.imageIds.length) {
+          report[id] = segReport;
+          continue;
+        }
+
+        const firstImageId = referencedVolume.imageIds[0];
+        const instance = OHIF.classes.MetadataProvider.get('instance', firstImageId);
+
+        if (!instance) {
+          report[id] = segReport;
+          continue;
+        }
+
+        report[id] = {
+          ...segReport,
+          PatientID: instance.PatientID ?? '000000',
+          PatientName: instance.PatientName.Alphabetic,
+          StudyInstanceUID: instance.StudyInstanceUID,
+          SeriesInstanceUID: instance.SeriesInstanceUID,
+          StudyDate: instance.StudyDate,
+        };
+      }
+
+      return report;
+    },
+    exportRTReportForAnnotations: ({ annotations }) => {
+      dicomRTAnnotationExport(annotations);
+    },
+    setFusionPTColormap: ({ toolGroupId, colormap }) => {
+      const toolGroup = toolGroupService.getToolGroup(toolGroupId);
+
+      if (!toolGroup) {
+        return;
+      }
+
+      const { viewportMatchDetails } = hangingProtocolService.getMatchDetails();
+
+      const ptDisplaySet = actions.getMatchingPTDisplaySet({
+        viewportMatchDetails,
+      });
+
+      if (!ptDisplaySet) {
+        return;
+      }
+
+      const fusionViewportIds = toolGroup.getViewportIds();
+
+      const viewports = [];
+      fusionViewportIds.forEach(viewportId => {
+        commandsManager.runCommand('setViewportColormap', {
+          viewportId,
+          displaySetInstanceUID: ptDisplaySet.displaySetInstanceUID,
+          colormap: {
+            name: colormap,
+          },
+        });
+
+        viewports.push(cornerstoneViewportService.getCornerstoneViewport(viewportId));
+      });
+
+      viewports.forEach(viewport => {
+        viewport.render();
+      });
+    },
+  };
+
+  const definitions = {
+    setEndSliceForROIThresholdTool: {
+      commandFn: actions.setEndSliceForROIThresholdTool,
+    },
+    setStartSliceForROIThresholdTool: {
+      commandFn: actions.setStartSliceForROIThresholdTool,
+    },
+    getMatchingPTDisplaySet: {
+      commandFn: actions.getMatchingPTDisplaySet,
+    },
+    getPTMetadata: {
+      commandFn: actions.getPTMetadata,
+    },
+    createNewLabelmapFromPT: {
+      commandFn: actions.createNewLabelmapFromPT,
+    },
+    thresholdSegmentationByRectangleROITool: {
+      commandFn: actions.thresholdSegmentationByRectangleROITool,
+    },
+    getTotalLesionGlycolysis: {
+      commandFn: actions.getTotalLesionGlycolysis,
+    },
+    calculateSuvPeak: {
+      commandFn: actions.calculateSuvPeak,
+    },
+    getLesionStats: {
+      commandFn: actions.getLesionStats,
+    },
+    calculateTMTV: {
+      commandFn: actions.calculateTMTV,
+    },
+    exportTMTVReportCSV: {
+      commandFn: actions.exportTMTVReportCSV,
+    },
+    createTMTVRTReport: {
+      commandFn: actions.createTMTVRTReport,
+    },
+    getSegmentationCSVReport: {
+      commandFn: actions.getSegmentationCSVReport,
+    },
+    exportRTReportForAnnotations: {
+      commandFn: actions.exportRTReportForAnnotations,
+    },
+    setFusionPTColormap: {
+      commandFn: actions.setFusionPTColormap,
+    },
+  };
+
+  return {
+    actions,
+    definitions,
+    defaultContext: 'TMTV:CORNERSTONE',
+  };
+};
+
+export default commandsModule;

extensions/tmtv/src/getHangingProtocolModule.ts

@@ -0,0 +1,350 @@
+import {
+  ctAXIAL,
+  ctCORONAL,
+  ctSAGITTAL,
+  fusionAXIAL,
+  fusionCORONAL,
+  fusionSAGITTAL,
+  mipSAGITTAL,
+  ptAXIAL,
+  ptCORONAL,
+  ptSAGITTAL,
+} from './utils/hpViewports';
+
+/**
+ * represents a 3x4 viewport layout configuration. The layout displays CT axial, sagittal, and coronal
+ * images in the first row, PT axial, sagittal, and coronal images in the second row, and fusion axial,
+ * sagittal, and coronal images in the third row. The fourth column is fully spanned by a MIP sagittal
+ * image, covering all three rows. It has synchronizers for windowLevel for all CT and PT images, and
+ * also camera synchronizer for each orientation
+ */
+const stage1: AppTypes.HangingProtocol.ProtocolStage = {
+  name: 'default',
+  id: 'default',
+  viewportStructure: {
+    layoutType: 'grid',
+    properties: {
+      rows: 3,
+      columns: 4,
+      layoutOptions: [
+        {
+          x: 0,
+          y: 0,
+          width: 1 / 4,
+          height: 1 / 3,
+        },
+        {
+          x: 1 / 4,
+          y: 0,
+          width: 1 / 4,
+          height: 1 / 3,
+        },
+        {
+          x: 2 / 4,
+          y: 0,
+          width: 1 / 4,
+          height: 1 / 3,
+        },
+        {
+          x: 0,
+          y: 1 / 3,
+          width: 1 / 4,
+          height: 1 / 3,
+        },
+        {
+          x: 1 / 4,
+          y: 1 / 3,
+          width: 1 / 4,
+          height: 1 / 3,
+        },
+        {
+          x: 2 / 4,
+          y: 1 / 3,
+          width: 1 / 4,
+          height: 1 / 3,
+        },
+        {
+          x: 0,
+          y: 2 / 3,
+          width: 1 / 4,
+          height: 1 / 3,
+        },
+        {
+          x: 1 / 4,
+          y: 2 / 3,
+          width: 1 / 4,
+          height: 1 / 3,
+        },
+        {
+          x: 2 / 4,
+          y: 2 / 3,
+          width: 1 / 4,
+          height: 1 / 3,
+        },
+        {
+          x: 3 / 4,
+          y: 0,
+          width: 1 / 4,
+          height: 1,
+        },
+      ],
+    },
+  },
+  viewports: [
+    ctAXIAL,
+    ctSAGITTAL,
+    ctCORONAL,
+    ptAXIAL,
+    ptSAGITTAL,
+    ptCORONAL,
+    fusionAXIAL,
+    fusionSAGITTAL,
+    fusionCORONAL,
+    mipSAGITTAL,
+  ],
+  createdDate: '2021-02-23T18:32:42.850Z',
+};
+
+/**
+ * The layout displays CT axial image in the top-left viewport, fusion axial image
+ * in the top-right viewport, PT axial image in the bottom-left viewport, and MIP
+ * sagittal image in the bottom-right viewport. The layout follows a simple grid
+ * pattern with 2 rows and 2 columns. It includes synchronizers as well.
+ */
+const stage2 = {
+  name: 'Fusion 2x2',
+  id: 'Fusion-2x2',
+  viewportStructure: {
+    layoutType: 'grid',
+    properties: {
+      rows: 2,
+      columns: 2,
+    },
+  },
+  viewports: [ctAXIAL, fusionAXIAL, ptAXIAL, mipSAGITTAL],
+};
+
+/**
+ * The top row displays CT images in axial, sagittal, and coronal orientations from
+ * left to right, respectively. The bottom row displays PT images in axial, sagittal,
+ * and coronal orientations from left to right, respectively.
+ * The layout follows a simple grid pattern with 2 rows and 3 columns.
+ * It includes synchronizers as well.
+ */
+const stage3: AppTypes.HangingProtocol.ProtocolStage = {
+  name: '2x3-layout',
+  id: '2x3-layout',
+  viewportStructure: {
+    layoutType: 'grid',
+    properties: {
+      rows: 2,
+      columns: 3,
+    },
+  },
+  viewports: [ctAXIAL, ctSAGITTAL, ctCORONAL, ptAXIAL, ptSAGITTAL, ptCORONAL],
+};
+
+/**
+ * In this layout, the top row displays PT images in coronal, sagittal, and axial
+ * orientations from left to right, respectively, followed by a MIP sagittal image
+ * that spans both rows on the rightmost side. The bottom row displays fusion images
+ * in coronal, sagittal, and axial orientations from left to right, respectively.
+ * There is no viewport in the bottom row's rightmost position, as the MIP sagittal viewport
+ * from the top row spans the full height of both rows.
+ * It includes synchronizers as well.
+ */
+const stage4: AppTypes.HangingProtocol.ProtocolStage = {
+  name: '2x4-layout',
+  id: '2x4-layout',
+  viewportStructure: {
+    layoutType: 'grid',
+    properties: {
+      rows: 2,
+      columns: 4,
+      layoutOptions: [
+        {
+          x: 0,
+          y: 0,
+          width: 1 / 4,
+          height: 1 / 2,
+        },
+        {
+          x: 1 / 4,
+          y: 0,
+          width: 1 / 4,
+          height: 1 / 2,
+        },
+        {
+          x: 2 / 4,
+          y: 0,
+          width: 1 / 4,
+          height: 1 / 2,
+        },
+        {
+          x: 3 / 4,
+          y: 0,
+          width: 1 / 4,
+          height: 1,
+        },
+        {
+          x: 0,
+          y: 1 / 2,
+          width: 1 / 4,
+          height: 1 / 2,
+        },
+        {
+          x: 1 / 4,
+          y: 1 / 2,
+          width: 1 / 4,
+          height: 1 / 2,
+        },
+        {
+          x: 2 / 4,
+          y: 1 / 2,
+          width: 1 / 4,
+          height: 1 / 2,
+        },
+      ],
+    },
+  },
+  viewports: [
+    ptCORONAL,
+    ptSAGITTAL,
+    ptAXIAL,
+    mipSAGITTAL,
+    fusionCORONAL,
+    fusionSAGITTAL,
+    fusionAXIAL,
+  ],
+};
+
+/**
+ * This layout displays three fusion viewports: axial, sagittal, and coronal.
+ * It follows a simple grid pattern with 1 row and 3 columns.
+ */
+// const stage0: AppTypes.HangingProtocol.ProtocolStage = {
+//   name: 'Fusion 1x3',
+//   viewportStructure: {
+//     layoutType: 'grid',
+//     properties: {
+//       rows: 1,
+//       columns: 3,
+//     },
+//   },
+//   viewports: [fusionAXIAL, fusionSAGITTAL, fusionCORONAL],
+// };
+
+const ptCT: AppTypes.HangingProtocol.Protocol = {
+  id: '@ohif/extension-tmtv.hangingProtocolModule.ptCT',
+  locked: true,
+  name: 'Default',
+  createdDate: '2021-02-23T19:22:08.894Z',
+  modifiedDate: '2022-10-04T19:22:08.894Z',
+  availableTo: {},
+  editableBy: {},
+  imageLoadStrategy: 'interleaveTopToBottom', // "default" , "interleaveTopToBottom",  "interleaveCenter"
+  protocolMatchingRules: [
+    {
+      attribute: 'ModalitiesInStudy',
+      constraint: {
+        contains: ['CT', 'PT'],
+      },
+    },
+    {
+      attribute: 'StudyDescription',
+      constraint: {
+        contains: 'PETCT',
+      },
+    },
+    {
+      attribute: 'StudyDescription',
+      constraint: {
+        contains: 'PET/CT',
+      },
+    },
+  ],
+  displaySetSelectors: {
+    ctDisplaySet: {
+      seriesMatchingRules: [
+        {
+          attribute: 'Modality',
+          constraint: {
+            equals: {
+              value: 'CT',
+            },
+          },
+          required: true,
+        },
+        {
+          attribute: 'isReconstructable',
+          constraint: {
+            equals: {
+              value: true,
+            },
+          },
+          required: true,
+        },
+        {
+          attribute: 'SeriesDescription',
+          constraint: {
+            contains: 'CT',
+          },
+        },
+        {
+          attribute: 'SeriesDescription',
+          constraint: {
+            contains: 'CT WB',
+          },
+        },
+      ],
+    },
+    ptDisplaySet: {
+      seriesMatchingRules: [
+        {
+          attribute: 'Modality',
+          constraint: {
+            equals: 'PT',
+          },
+          required: true,
+        },
+        {
+          attribute: 'isReconstructable',
+          constraint: {
+            equals: {
+              value: true,
+            },
+          },
+          required: true,
+        },
+        {
+          attribute: 'SeriesDescription',
+          constraint: {
+            contains: 'Corrected',
+          },
+        },
+        {
+          weight: 2,
+          attribute: 'SeriesDescription',
+          constraint: {
+            doesNotContain: {
+              value: 'Uncorrected',
+            },
+          },
+        },
+      ],
+    },
+  },
+  stages: [stage1, stage2, stage3, stage4],
+  numberOfPriorsReferenced: -1,
+};
+
+function getHangingProtocolModule() {
+  return [
+    {
+      name: ptCT.id,
+      protocol: ptCT,
+    },
+  ];
+}
+
+export default getHangingProtocolModule;

extensions/tmtv/src/getPanelModule.tsx

@@ -0,0 +1,91 @@
+import React from 'react';
+import { PanelPetSUV, PanelROIThresholdExport } from './Panels';
+import { Toolbox } from '@ohif/ui-next';
+import PanelTMTV from './Panels/PanelTMTV';
+
+function getPanelModule({ commandsManager, extensionManager, servicesManager }) {
+  const wrappedPanelPetSuv = () => {
+    return (
+      <PanelPetSUV
+        commandsManager={commandsManager}
+        servicesManager={servicesManager}
+        extensionManager={extensionManager}
+      />
+    );
+  };
+
+  const wrappedROIThresholdToolbox = () => {
+    return (
+      <Toolbox
+        commandsManager={commandsManager}
+        servicesManager={servicesManager}
+        extensionManager={extensionManager}
+        buttonSectionId="ROIThresholdToolbox"
+        title="Threshold Tools"
+      />
+    );
+  };
+
+  const wrappedROIThresholdExport = () => {
+    return (
+      <PanelROIThresholdExport
+        commandsManager={commandsManager}
+        servicesManager={servicesManager}
+      />
+    );
+  };
+
+  const wrappedPanelTMTV = () => {
+    return (
+      <>
+        <Toolbox
+          commandsManager={commandsManager}
+          servicesManager={servicesManager}
+          extensionManager={extensionManager}
+          buttonSectionId="ROIThresholdToolbox"
+          title="Threshold Tools"
+        />
+        <PanelTMTV
+          commandsManager={commandsManager}
+          servicesManager={servicesManager}
+        />
+        <PanelROIThresholdExport
+          commandsManager={commandsManager}
+          servicesManager={servicesManager}
+        />
+      </>
+    );
+  };
+
+  return [
+    {
+      name: 'petSUV',
+      iconName: 'tab-patient-info',
+      iconLabel: 'Patient Info',
+      label: 'Patient Info',
+      component: wrappedPanelPetSuv,
+    },
+    {
+      name: 'tmtv',
+      iconName: 'tab-segmentation',
+      iconLabel: 'Segmentation',
+      component: wrappedPanelTMTV,
+    },
+    {
+      name: 'tmtvBox',
+      iconName: 'tab-segmentation',
+      iconLabel: 'Segmentation',
+      label: 'Segmentation Toolbox',
+      component: wrappedROIThresholdToolbox,
+    },
+    {
+      name: 'tmtvExport',
+      iconName: 'tab-segmentation',
+      iconLabel: 'Segmentation',
+      label: 'Segmentation Export',
+      component: wrappedROIThresholdExport,
+    },
+  ];
+}
+
+export default getPanelModule;

extensions/tmtv/src/getToolbarModule.tsx

@@ -0,0 +1,10 @@
+import RectangleROIOptions from './Panels/RectangleROIOptions';
+
+export default function getToolbarModule({ commandsManager, servicesManager }) {
+  return [
+    {
+      name: 'tmtv.RectangleROIThresholdOptions',
+      defaultComponent: () => RectangleROIOptions({ commandsManager, servicesManager }),
+    },
+  ];
+}

extensions/tmtv/src/id.js

@@ -0,0 +1,5 @@
+import packageJson from '../package.json';
+
+const id = packageJson.name;
+
+export { id };

extensions/tmtv/src/index.tsx

@@ -0,0 +1,31 @@
+import { id } from './id';
+import getHangingProtocolModule from './getHangingProtocolModule';
+import getPanelModule from './getPanelModule';
+import init from './init';
+import commandsModule from './commandsModule';
+import getToolbarModule from './getToolbarModule';
+
+/**
+ *
+ */
+const tmtvExtension = {
+  /**
+   * Only required property. Should be a unique value across all extensions.
+   */
+  id,
+  preRegistration({ servicesManager, commandsManager, extensionManager, configuration = {} }) {
+    init({ servicesManager, commandsManager, extensionManager, configuration });
+  },
+  getToolbarModule,
+  getPanelModule,
+  getHangingProtocolModule,
+  getCommandsModule({ servicesManager, commandsManager, extensionManager }) {
+    return commandsModule({
+      servicesManager,
+      commandsManager,
+      extensionManager,
+    });
+  },
+};
+
+export default tmtvExtension;

extensions/tmtv/src/init.js

@@ -0,0 +1,52 @@
+import {
+  addTool,
+  RectangleROIStartEndThresholdTool,
+  CircleROIStartEndThresholdTool,
+} from '@cornerstonejs/tools';
+import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
+
+import measurementServiceMappingsFactory from './utils/measurementServiceMappings/measurementServiceMappingsFactory';
+
+const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
+
+/**
+ *
+ * @param {Object} servicesManager
+ * @param {Object} configuration
+ * @param {Object|Array} configuration.csToolsConfig
+ */
+export default function init({ servicesManager }) {
+  const { measurementService, displaySetService, cornerstoneViewportService } =
+    servicesManager.services;
+
+  addTool(RectangleROIStartEndThresholdTool);
+  addTool(CircleROIStartEndThresholdTool);
+
+  const { RectangleROIStartEndThreshold, CircleROIStartEndThreshold } =
+    measurementServiceMappingsFactory(
+      measurementService,
+      displaySetService,
+      cornerstoneViewportService
+    );
+
+  const csTools3DVer1MeasurementSource = measurementService.getSource(
+    CORNERSTONE_3D_TOOLS_SOURCE_NAME,
+    CORNERSTONE_3D_TOOLS_SOURCE_VERSION
+  );
+
+  measurementService.addMapping(
+    csTools3DVer1MeasurementSource,
+    'RectangleROIStartEndThreshold',
+    RectangleROIStartEndThreshold.matchingCriteria,
+    RectangleROIStartEndThreshold.toAnnotation,
+    RectangleROIStartEndThreshold.toMeasurement
+  );
+
+  measurementService.addMapping(
+    csTools3DVer1MeasurementSource,
+    'CircleROIStartEndThreshold',
+    CircleROIStartEndThreshold.matchingCriteria,
+    CircleROIStartEndThreshold.toAnnotation,
+    CircleROIStartEndThreshold.toMeasurement
+  );
+}

extensions/tmtv/src/utils/calculateSUVPeakWorker.js

@@ -0,0 +1,209 @@
+import { utilities } from '@cornerstonejs/core';
+import { utilities as cstUtils } from '@cornerstonejs/tools';
+import { vec3 } from 'gl-matrix';
+import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
+import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
+import { expose } from 'comlink';
+
+const createVolume = ({ dimensions, origin, direction, spacing, metadata, scalarData }) => {
+  const imageData = vtkImageData.newInstance();
+  imageData.setDimensions(dimensions);
+  imageData.setOrigin(origin);
+  imageData.setDirection(direction);
+  imageData.setSpacing(spacing);
+
+  const scalarArray = vtkDataArray.newInstance({
+    name: 'Pixels',
+    numberOfComponents: 1,
+    values: scalarData,
+  });
+
+  imageData.getPointData().setScalars(scalarArray);
+
+  imageData.modified();
+
+  const voxelManager = utilities.VoxelManager.createScalarVolumeVoxelManager({
+    scalarData,
+    dimensions,
+    numberOfComponents: 1,
+  });
+  return {
+    imageData,
+    spacing,
+    origin,
+    direction,
+    metadata,
+    voxelManager,
+  };
+};
+
+/**
+ * This method calculates the SUV peak on a segmented ROI from a reference PET
+ * volume. If a rectangle annotation is provided, the peak is calculated within that
+ * rectangle. Otherwise, the calculation is performed on the entire volume which
+ * will be slower but same result.
+ * @param viewport Viewport to use for the calculation
+ * @param labelmap Labelmap from which the mask is taken
+ * @param referenceVolume PET volume to use for SUV calculation
+ * @param toolData [Optional] list of toolData to use for SUV calculation
+ * @param segmentIndex The index of the segment to use for masking
+ * @returns
+ */
+function calculateSuvPeak({ labelmapProps, referenceVolumeProps, annotations, segmentIndex = 1 }) {
+  const labelmapInfo = createVolume(labelmapProps);
+  const referenceInfo = createVolume(referenceVolumeProps);
+
+  if (referenceInfo.metadata.Modality !== 'PT') {
+    return;
+  }
+
+  const { dimensions, imageData: labelmapImageData } = labelmapInfo;
+  const { imageData: referenceVolumeImageData } = referenceInfo;
+
+  let boundsIJK;
+  // Todo: using the first annotation for now
+  if (annotations?.length && annotations[0].data?.cachedStats) {
+    const { projectionPoints } = annotations[0].data.cachedStats;
+    const pointsToUse = [].concat(...projectionPoints); // cannot use flat() because of typescript compiler right now
+
+    const rectangleCornersIJK = pointsToUse.map(world => {
+      const ijk = vec3.fromValues(0, 0, 0);
+      referenceVolumeImageData.worldToIndex(world, ijk);
+      return ijk;
+    });
+
+    boundsIJK = cstUtils.boundingBox.getBoundingBoxAroundShape(rectangleCornersIJK, dimensions);
+  }
+
+  let max = 0;
+  let maxIJK = [0, 0, 0];
+  let maxLPS = [0, 0, 0];
+
+  const callback = ({ pointIJK, pointLPS }) => {
+    const value = labelmapInfo.voxelManager.getAtIJKPoint(pointIJK);
+
+    if (value !== segmentIndex) {
+      return;
+    }
+
+    const referenceValue = referenceInfo.voxelManager.getAtIJKPoint(pointIJK);
+
+    if (referenceValue > max) {
+      max = referenceValue;
+      maxIJK = pointIJK;
+      maxLPS = pointLPS;
+    }
+  };
+
+  labelmapInfo.voxelManager.forEach(callback, {
+    boundsIJK,
+    imageData: labelmapImageData,
+    isInObject: () => true,
+    returnPoints: true,
+  });
+
+  const direction = labelmapImageData.getDirection().slice(0, 3);
+
+  /**
+   * 2. Find the bottom and top of the great circle for the second sphere (1cc sphere)
+   * V = (4/3)πr3
+   */
+  const radius = Math.pow(1 / ((4 / 3) * Math.PI), 1 / 3) * 10;
+  const diameter = radius * 2;
+
+  const secondaryCircleWorld = vec3.create();
+  const bottomWorld = vec3.create();
+  const topWorld = vec3.create();
+  referenceVolumeImageData.indexToWorld(maxIJK, secondaryCircleWorld);
+  vec3.scaleAndAdd(bottomWorld, secondaryCircleWorld, direction, -diameter / 2);
+  vec3.scaleAndAdd(topWorld, secondaryCircleWorld, direction, diameter / 2);
+  const suvPeakCirclePoints = [bottomWorld, topWorld];
+
+  /**
+   * 3. Find the Mean and Max of the 1cc sphere centered on the suv Max of the previous
+   * sphere
+   */
+  let count = 0;
+  let acc = 0;
+  const suvPeakMeanCallback = ({ value }) => {
+    acc += value;
+    count += 1;
+  };
+
+  cstUtils.pointInSurroundingSphereCallback(
+    referenceVolumeImageData,
+    suvPeakCirclePoints,
+    suvPeakMeanCallback
+  );
+
+  const mean = acc / count;
+
+  return {
+    max,
+    maxIJK,
+    maxLPS,
+    mean,
+  };
+}
+
+function calculateTMTV(labelmapProps, segmentIndex = 1) {
+  const labelmaps = labelmapProps.map(props => createVolume(props));
+
+  const mergedLabelmap =
+    labelmaps.length === 1
+      ? labelmaps[0]
+      : cstUtils.segmentation.createMergedLabelmapForIndex(labelmaps);
+
+  const { imageData, spacing } = mergedLabelmap;
+  const values = imageData.getPointData().getScalars().getData();
+
+  // count non-zero values inside the outputData, this would
+  // consider the overlapping regions to be only counted once
+  const numVoxels = values.reduce((acc, curr) => {
+    if (curr > 0) {
+      return acc + 1;
+    }
+    return acc;
+  }, 0);
+
+  return 1e-3 * numVoxels * spacing[0] * spacing[1] * spacing[2];
+}
+
+function getTotalLesionGlycolysis({ labelmapProps, referenceVolumeProps }) {
+  const labelmaps = labelmapProps.map(props => createVolume(props));
+
+  const mergedLabelmap =
+    labelmaps.length === 1
+      ? labelmaps[0]
+      : cstUtils.segmentation.createMergedLabelmapForIndex(labelmaps);
+
+  // grabbing the first labelmap referenceVolume since it will be the same for all
+  const { spacing } = labelmaps[0];
+
+  const ptVolume = createVolume(referenceVolumeProps);
+
+  let suv = 0;
+  let totalLesionVoxelCount = 0;
+  const scalarDataLength = mergedLabelmap.voxelManager.getScalarDataLength();
+  for (let i = 0; i < scalarDataLength; i++) {
+    // if not background
+    if (mergedLabelmap.voxelManager.getAtIndex(i) !== 0) {
+      suv += ptVolume.voxelManager.getAtIndex(i);
+      totalLesionVoxelCount += 1;
+    }
+  }
+
+  // Average SUV for the merged labelmap
+  const averageSuv = suv / totalLesionVoxelCount;
+
+  // total Lesion Glycolysis [suv * ml]
+  return averageSuv * totalLesionVoxelCount * spacing[0] * spacing[1] * spacing[2] * 1e-3;
+}
+
+const obj = {
+  calculateSuvPeak,
+  calculateTMTV,
+  getTotalLesionGlycolysis,
+};
+
+expose(obj);

extensions/tmtv/src/utils/calculateTMTV.ts

@@ -0,0 +1,42 @@
+import { Types } from '@cornerstonejs/core';
+import { utilities } from '@cornerstonejs/tools';
+
+/**
+ * Given a list of labelmaps (with the possibility of overlapping regions),
+ * and a referenceVolume, it calculates the total metabolic tumor volume (TMTV)
+ * by flattening and rasterizing each segment into a single labelmap and summing
+ * the total number of volume voxels. It should be noted that for this calculation
+ * we do not double count voxels that are part of multiple labelmaps.
+ * @param {} labelmaps
+ * @param {number} segmentIndex
+ * @returns {number} TMTV in ml
+ */
+function calculateTMTV(labelmaps: Array<Types.IImageVolume>, segmentIndex = 1): number {
+  const volumeId = 'mergedLabelmap';
+
+  const mergedLabelmap = utilities.segmentation.createMergedLabelmapForIndex(
+    labelmaps,
+    segmentIndex,
+    volumeId
+  );
+
+  const { imageData, spacing, voxelManager } = mergedLabelmap;
+
+  // count non-zero values inside the outputData, this would
+  // consider the overlapping regions to be only counted once
+  let numVoxels = 0;
+  const callback = ({ value }) => {
+    if (value > 0) {
+      numVoxels += 1;
+    }
+  };
+
+  voxelManager.forEach(callback, {
+    imageData,
+    isInObject: () => true,
+  });
+
+  return 1e-3 * numVoxels * spacing[0] * spacing[1] * spacing[2];
+}
+
+export default calculateTMTV;

extensions/tmtv/src/utils/createAndDownloadTMTVReport.js

@@ -0,0 +1,45 @@
+export default function createAndDownloadTMTVReport(segReport, additionalReportRows, options = {}) {
+  const firstReport = segReport[Object.keys(segReport)[0]];
+  const columns = Object.keys(firstReport);
+  const csv = [columns.join(',')];
+
+  Object.values(segReport).forEach(segmentation => {
+    const row = [];
+    columns.forEach(column => {
+      // if it is array then we need to replace , with space to avoid csv parsing error
+      row.push(
+        Array.isArray(segmentation[column]) ? segmentation[column].join(' ') : segmentation[column]
+      );
+    });
+    csv.push(row.join(','));
+  });
+
+  csv.push('');
+  csv.push('');
+  csv.push('');
+
+  csv.push(`Patient ID,${firstReport.PatientID}`);
+  csv.push(`Study Date,${firstReport.StudyDate}`);
+  csv.push('');
+  additionalReportRows.forEach(({ key, value: values }) => {
+    const temp = [];
+    temp.push(`${key}`);
+    Object.keys(values).forEach(k => {
+      temp.push(`${k}`);
+      temp.push(`${values[k]}`);
+    });
+
+    csv.push(temp.join(','));
+  });
+
+  const blob = new Blob([csv.join('\n')], {
+    type: 'text/csv;charset=utf-8',
+  });
+
+  const url = URL.createObjectURL(blob);
+
+  const a = document.createElement('a');
+  a.href = url;
+  a.download = options.filename ?? `${firstReport.PatientID}_tmtv.csv`;
+  a.click();
+}

extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/dicomRTAnnotationExport.js

@@ -0,0 +1,19 @@
+import dcmjs from 'dcmjs';
+import { classes, DicomMetadataStore } from '@ohif/core';
+import { adaptersRT } from '@cornerstonejs/adapters';
+
+const { datasetToBlob } = dcmjs.data;
+const metadataProvider = classes.MetadataProvider;
+
+export default function dicomRTAnnotationExport(annotations) {
+  const dataset = adaptersRT.Cornerstone3D.RTSS.generateRTSSFromAnnotations(
+    annotations,
+    metadataProvider,
+    DicomMetadataStore
+  );
+  const reportBlob = datasetToBlob(dataset);
+
+  //Create a URL for the binary.
+  var objectUrl = URL.createObjectURL(reportBlob);
+  window.location.assign(objectUrl);
+}

extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/index.js

@@ -0,0 +1,3 @@
+import dicomRTAnnotationExport from './dicomRTAnnotationExport';
+
+export default dicomRTAnnotationExport;

extensions/tmtv/src/utils/getThresholdValue.ts

@@ -0,0 +1,73 @@
+import * as csTools from '@cornerstonejs/tools';
+
+function getRoiStats(referencedVolume, annotations) {
+  // roiStats
+  const { imageData } = referencedVolume;
+  const values = imageData.getPointData().getScalars().getData();
+
+  // Todo: add support for other strategies
+  const { fn, baseValue } = _getStrategyFn('max');
+  let value = baseValue;
+
+  const boundsIJK = csTools.utilities.rectangleROITool.getBoundsIJKFromRectangleAnnotations(
+    annotations,
+    referencedVolume
+  );
+
+  const [[iMin, iMax], [jMin, jMax], [kMin, kMax]] = boundsIJK;
+
+  for (let i = iMin; i <= iMax; i++) {
+    for (let j = jMin; j <= jMax; j++) {
+      for (let k = kMin; k <= kMax; k++) {
+        const offset = imageData.computeOffsetIndex([i, j, k]);
+        value = fn(values[offset], value);
+      }
+    }
+  }
+  return value;
+}
+
+function getThresholdValues(
+  annotationUIDs,
+  referencedVolumes,
+  config
+): { ptLower: number; ptUpper: number; ctLower: number; ctUpper: number } {
+  if (config.strategy === 'range') {
+    return {
+      ptLower: Number(config.ptLower),
+      ptUpper: Number(config.ptUpper),
+      ctLower: Number(config.ctLower),
+      ctUpper: Number(config.ctUpper),
+    };
+  }
+
+  const { weight } = config;
+  const annotations = annotationUIDs.map(annotationUID =>
+    csTools.annotation.state.getAnnotation(annotationUID)
+  );
+
+  const ptValue = getRoiStats(referencedVolumes[0], annotations);
+
+  return {
+    ctLower: -Infinity,
+    ctUpper: +Infinity,
+    ptLower: weight * ptValue,
+    ptUpper: +Infinity,
+  };
+}
+
+function _getStrategyFn(statistic): {
+  fn: (a: number, b: number) => number;
+  baseValue: number;
+} {
+  const baseValue = -Infinity;
+  const fn = (number, maxValue) => {
+    if (number > maxValue) {
+      maxValue = number;
+    }
+    return maxValue;
+  };
+  return { fn, baseValue };
+}
+
+export default getThresholdValues;

extensions/tmtv/src/utils/handleROIThresholding.ts

@@ -0,0 +1,97 @@
+import { Segment, Segmentation } from '@cornerstonejs/tools/types';
+import { triggerEvent, eventTarget, Enums } from '@cornerstonejs/core';
+
+export const handleROIThresholding = async ({
+  segmentationId,
+  commandsManager,
+  segmentationService,
+}: withAppTypes<{
+  segmentationId: string;
+}>) => {
+  const segmentation = segmentationService.getSegmentation(segmentationId);
+
+  triggerEvent(eventTarget, Enums.Events.WEB_WORKER_PROGRESS, {
+    progress: 0,
+    type: 'Calculate Lesion Stats',
+    id: segmentationId,
+  });
+
+  // re-calculating the cached stats for the active segmentation
+  const updatedPerSegmentCachedStats = {};
+  for (const [segmentIndex, segment] of Object.entries(segmentation.segments)) {
+    if (!segment) {
+      continue;
+    }
+
+    const numericSegmentIndex = Number(segmentIndex);
+
+    const lesionStats = await commandsManager.run('getLesionStats', {
+      segmentationId,
+      segmentIndex: numericSegmentIndex,
+    });
+
+    const suvPeak = await commandsManager.run('calculateSuvPeak', {
+      segmentationId,
+      segmentIndex: numericSegmentIndex,
+    });
+
+    const lesionGlyoclysisStats = lesionStats.volume * lesionStats.meanValue;
+
+    // update segDetails with the suv peak for the active segmentation
+    const cachedStats = {
+      lesionStats,
+      suvPeak,
+      lesionGlyoclysisStats,
+    };
+
+    const updatedSegment: Segment = {
+      ...segment,
+      cachedStats: {
+        ...segment.cachedStats,
+        ...cachedStats,
+      },
+    };
+
+    updatedPerSegmentCachedStats[numericSegmentIndex] = cachedStats;
+
+    segmentation.segments[segmentIndex] = updatedSegment;
+  }
+
+  // all available segmentations
+  const segmentations = segmentationService.getSegmentations();
+  const tmtv = await commandsManager.run('calculateTMTV', { segmentations });
+
+  triggerEvent(eventTarget, Enums.Events.WEB_WORKER_PROGRESS, {
+    progress: 100,
+    type: 'Calculate Lesion Stats',
+    id: segmentationId,
+  });
+
+  // add the tmtv to all the segment cachedStats, although it is a global
+  // value but we don't have any other way to display it for now
+  // Update all segmentations with the calculated TMTV
+  segmentations.forEach(segmentation => {
+    segmentation.cachedStats = {
+      ...segmentation.cachedStats,
+      tmtv,
+    };
+
+    // Update each segment within the segmentation
+    Object.keys(segmentation.segments).forEach(segmentIndex => {
+      segmentation.segments[segmentIndex].cachedStats = {
+        ...segmentation.segments[segmentIndex].cachedStats,
+        tmtv,
+      };
+    });
+
+    // Update the segmentation object
+    const updatedSegmentation: Segmentation = {
+      ...segmentation,
+      segments: {
+        ...segmentation.segments,
+      },
+    };
+
+    segmentationService.addOrUpdateSegmentation(updatedSegmentation);
+  });
+};

extensions/tmtv/src/utils/hpViewports.ts

@@ -0,0 +1,494 @@
+// Common sync group configurations
+const cameraPositionSync = (id: string) => ({
+  type: 'cameraPosition',
+  id,
+  source: true,
+  target: true,
+});
+
+const hydrateSegSync = {
+  type: 'hydrateseg',
+  id: 'sameFORId',
+  source: true,
+  target: true,
+  options: {
+    matchingRules: ['sameFOR'],
+  },
+};
+
+const ctAXIAL: AppTypes.HangingProtocol.Viewport = {
+  viewportOptions: {
+    viewportId: 'ctAXIAL',
+    viewportType: 'volume',
+    orientation: 'axial',
+    toolGroupId: 'ctToolGroup',
+    initialImageOptions: {
+      // index: 5,
+      preset: 'first', // 'first', 'last', 'middle'
+    },
+    syncGroups: [
+      cameraPositionSync('axialSync'),
+      {
+        type: 'voi',
+        id: 'ctWLSync',
+        source: true,
+        target: true,
+        options: {
+          syncColormap: true,
+        },
+      },
+      hydrateSegSync,
+    ],
+  },
+  displaySets: [
+    {
+      id: 'ctDisplaySet',
+    },
+  ],
+};
+
+const ctSAGITTAL: AppTypes.HangingProtocol.Viewport = {
+  viewportOptions: {
+    viewportId: 'ctSAGITTAL',
+    viewportType: 'volume',
+    orientation: 'sagittal',
+    toolGroupId: 'ctToolGroup',
+    syncGroups: [
+      cameraPositionSync('sagittalSync'),
+      {
+        type: 'voi',
+        id: 'ctWLSync',
+        source: true,
+        target: true,
+        options: {
+          syncColormap: true,
+        },
+      },
+      hydrateSegSync,
+    ],
+  },
+  displaySets: [
+    {
+      id: 'ctDisplaySet',
+    },
+  ],
+};
+
+const ctCORONAL: AppTypes.HangingProtocol.Viewport = {
+  viewportOptions: {
+    viewportId: 'ctCORONAL',
+    viewportType: 'volume',
+    orientation: 'coronal',
+    toolGroupId: 'ctToolGroup',
+    syncGroups: [
+      cameraPositionSync('coronalSync'),
+      {
+        type: 'voi',
+        id: 'ctWLSync',
+        source: true,
+        target: true,
+        options: {
+          syncColormap: true,
+        },
+      },
+      hydrateSegSync,
+    ],
+  },
+  displaySets: [
+    {
+      id: 'ctDisplaySet',
+    },
+  ],
+};
+
+const ptAXIAL: AppTypes.HangingProtocol.Viewport = {
+  viewportOptions: {
+    viewportId: 'ptAXIAL',
+    viewportType: 'volume',
+    background: [1, 1, 1],
+    orientation: 'axial',
+    toolGroupId: 'ptToolGroup',
+    initialImageOptions: {
+      // index: 5,
+      preset: 'first', // 'first', 'last', 'middle'
+    },
+    syncGroups: [
+      cameraPositionSync('axialSync'),
+      {
+        type: 'voi',
+        id: 'ptWLSync',
+        source: true,
+        target: true,
+        options: {
+          syncColormap: true,
+        },
+      },
+      {
+        type: 'voi',
+        id: 'ptFusionWLSync',
+        source: true,
+        target: false,
+        options: {
+          syncColormap: false,
+          syncInvertState: false,
+        },
+      },
+      hydrateSegSync,
+    ],
+  },
+  displaySets: [
+    {
+      options: {
+        voi: {
+          custom: 'getPTVOIRange',
+        },
+        voiInverted: true,
+      },
+      id: 'ptDisplaySet',
+    },
+  ],
+};
+
+const ptSAGITTAL: AppTypes.HangingProtocol.Viewport = {
+  viewportOptions: {
+    viewportId: 'ptSAGITTAL',
+    viewportType: 'volume',
+    orientation: 'sagittal',
+    background: [1, 1, 1],
+    toolGroupId: 'ptToolGroup',
+    syncGroups: [
+      cameraPositionSync('sagittalSync'),
+      {
+        type: 'voi',
+        id: 'ptWLSync',
+        source: true,
+        target: true,
+        options: {
+          syncColormap: true,
+        },
+      },
+      {
+        type: 'voi',
+        id: 'ptFusionWLSync',
+        source: true,
+        target: false,
+        options: {
+          syncColormap: false,
+          syncInvertState: false,
+        },
+      },
+      hydrateSegSync,
+    ],
+  },
+  displaySets: [
+    {
+      options: {
+        voi: {
+          custom: 'getPTVOIRange',
+        },
+        voiInverted: true,
+      },
+      id: 'ptDisplaySet',
+    },
+  ],
+};
+
+const ptCORONAL: AppTypes.HangingProtocol.Viewport = {
+  viewportOptions: {
+    viewportId: 'ptCORONAL',
+    viewportType: 'volume',
+    orientation: 'coronal',
+    background: [1, 1, 1],
+    toolGroupId: 'ptToolGroup',
+    syncGroups: [
+      cameraPositionSync('coronalSync'),
+      {
+        type: 'voi',
+        id: 'ptWLSync',
+        source: true,
+        target: true,
+        options: {
+          syncColormap: true,
+        },
+      },
+      {
+        type: 'voi',
+        id: 'ptFusionWLSync',
+        source: true,
+        target: false,
+        options: {
+          syncColormap: false,
+          syncInvertState: false,
+        },
+      },
+      hydrateSegSync,
+    ],
+  },
+  displaySets: [
+    {
+      options: {
+        voi: {
+          custom: 'getPTVOIRange',
+        },
+        voiInverted: true,
+      },
+      id: 'ptDisplaySet',
+    },
+  ],
+};
+
+const fusionAXIAL: AppTypes.HangingProtocol.Viewport = {
+  viewportOptions: {
+    viewportId: 'fusionAXIAL',
+    viewportType: 'volume',
+    orientation: 'axial',
+    toolGroupId: 'fusionToolGroup',
+    initialImageOptions: {
+      // index: 5,
+      preset: 'first', // 'first', 'last', 'middle'
+    },
+    syncGroups: [
+      cameraPositionSync('axialSync'),
+      {
+        type: 'voi',
+        id: 'ctWLSync',
+        source: false,
+        target: true,
+      },
+      {
+        type: 'voi',
+        id: 'fusionWLSync',
+        source: true,
+        target: true,
+        options: {
+          syncColormap: true,
+        },
+      },
+      {
+        type: 'voi',
+        id: 'ptFusionWLSync',
+        source: false,
+        target: true,
+        options: {
+          syncColormap: false,
+          syncInvertState: false,
+        },
+      },
+      hydrateSegSync,
+    ],
+  },
+  displaySets: [
+    {
+      id: 'ctDisplaySet',
+    },
+    {
+      id: 'ptDisplaySet',
+      options: {
+        colormap: {
+          name: 'hsv',
+          opacity: [
+            { value: 0, opacity: 0 },
+            { value: 0.1, opacity: 0.8 },
+            { value: 1, opacity: 0.9 },
+          ],
+        },
+        voi: {
+          custom: 'getPTVOIRange',
+        },
+      },
+    },
+  ],
+};
+
+const fusionSAGITTAL = {
+  viewportOptions: {
+    viewportId: 'fusionSAGITTAL',
+    viewportType: 'volume',
+    orientation: 'sagittal',
+    toolGroupId: 'fusionToolGroup',
+    // initialImageOptions: {
+    //   index: 180,
+    //   preset: 'middle', // 'first', 'last', 'middle'
+    // },
+    syncGroups: [
+      cameraPositionSync('sagittalSync'),
+      {
+        type: 'voi',
+        id: 'ctWLSync',
+        source: false,
+        target: true,
+      },
+      {
+        type: 'voi',
+        id: 'fusionWLSync',
+        source: true,
+        target: true,
+        options: {
+          syncColormap: true,
+        },
+      },
+      {
+        type: 'voi',
+        id: 'ptFusionWLSync',
+        source: false,
+        target: true,
+        options: {
+          syncColormap: false,
+          syncInvertState: false,
+        },
+      },
+      hydrateSegSync,
+    ],
+  },
+  displaySets: [
+    {
+      id: 'ctDisplaySet',
+    },
+    {
+      id: 'ptDisplaySet',
+      options: {
+        colormap: {
+          name: 'hsv',
+          opacity: [
+            { value: 0, opacity: 0 },
+            { value: 0.1, opacity: 0.8 },
+            { value: 1, opacity: 0.9 },
+          ],
+        },
+        voi: {
+          custom: 'getPTVOIRange',
+        },
+      },
+    },
+  ],
+};
+
+const fusionCORONAL = {
+  viewportOptions: {
+    viewportId: 'fusionCoronal',
+    viewportType: 'volume',
+    orientation: 'coronal',
+    toolGroupId: 'fusionToolGroup',
+    // initialImageOptions: {
+    //   index: 180,
+    //   preset: 'middle', // 'first', 'last', 'middle'
+    // },
+    syncGroups: [
+      cameraPositionSync('coronalSync'),
+      {
+        type: 'voi',
+        id: 'ctWLSync',
+        source: false,
+        target: true,
+      },
+      {
+        type: 'voi',
+        id: 'fusionWLSync',
+        source: true,
+        target: true,
+        options: {
+          syncColormap: true,
+        },
+      },
+      {
+        type: 'voi',
+        id: 'ptFusionWLSync',
+        source: false,
+        target: true,
+        options: {
+          syncColormap: false,
+          syncInvertState: false,
+        },
+      },
+      hydrateSegSync,
+    ],
+  },
+  displaySets: [
+    {
+      id: 'ctDisplaySet',
+    },
+    {
+      id: 'ptDisplaySet',
+      options: {
+        colormap: {
+          name: 'hsv',
+          opacity: [
+            { value: 0, opacity: 0 },
+            { value: 0.1, opacity: 0.8 },
+            { value: 1, opacity: 0.9 },
+          ],
+        },
+        voi: {
+          custom: 'getPTVOIRange',
+        },
+      },
+    },
+  ],
+};
+
+const mipSAGITTAL: AppTypes.HangingProtocol.Viewport = {
+  viewportOptions: {
+    viewportId: 'mipSagittal',
+    viewportType: 'volume',
+    orientation: 'sagittal',
+    background: [1, 1, 1],
+    toolGroupId: 'mipToolGroup',
+    syncGroups: [
+      {
+        type: 'voi',
+        id: 'ptWLSync',
+        source: true,
+        target: true,
+        options: {
+          syncColormap: true,
+        },
+      },
+      {
+        type: 'voi',
+        id: 'ptFusionWLSync',
+        source: true,
+        target: false,
+        options: {
+          syncColormap: false,
+          syncInvertState: false,
+        },
+      },
+      hydrateSegSync,
+    ],
+
+    // Custom props can be used to set custom properties which extensions
+    // can react on.
+    customViewportProps: {
+      // We use viewportDisplay to filter the viewports which are displayed
+      // in mip and we set the scrollbar according to their rotation index
+      // in the cornerstone extension.
+      hideOverlays: true,
+    },
+  },
+  displaySets: [
+    {
+      options: {
+        blendMode: 'MIP',
+        slabThickness: 'fullVolume',
+        voi: {
+          custom: 'getPTVOIRange',
+        },
+        voiInverted: true,
+      },
+      id: 'ptDisplaySet',
+    },
+  ],
+};
+
+export {
+  ctAXIAL,
+  ctSAGITTAL,
+  ctCORONAL,
+  ptAXIAL,
+  ptSAGITTAL,
+  ptCORONAL,
+  fusionAXIAL,
+  fusionSAGITTAL,
+  fusionCORONAL,
+  mipSAGITTAL,
+};

extensions/tmtv/src/utils/measurementServiceMappings/CircleROIStartEndThreshold.js

@@ -0,0 +1,67 @@
+import SUPPORTED_TOOLS from './constants/supportedTools';
+import { getSOPInstanceAttributes } from '@ohif/extension-cornerstone';
+
+const CircleROIStartEndThreshold = {
+  toAnnotation: (measurement, definition) => {},
+
+  /**
+   * Maps cornerstone annotation event data to measurement service format.
+   *
+   * @param {Object} cornerstone Cornerstone event data
+   * @return {Measurement} Measurement instance
+   */
+  toMeasurement: (csToolsEventDetail, displaySetService, cornerstoneViewportService) => {
+    const { annotation, viewportId } = csToolsEventDetail;
+    const { metadata, data, annotationUID } = annotation;
+
+    if (!metadata || !data) {
+      console.warn('Length tool: Missing metadata or data');
+      return null;
+    }
+
+    const { toolName, referencedImageId, FrameOfReferenceUID } = metadata;
+    const validToolType = SUPPORTED_TOOLS.includes(toolName);
+
+    if (!validToolType) {
+      throw new Error('Tool not supported');
+    }
+
+    const { SOPInstanceUID, SeriesInstanceUID, StudyInstanceUID } = getSOPInstanceAttributes(
+      referencedImageId,
+      cornerstoneViewportService,
+      viewportId
+    );
+
+    let displaySet;
+
+    if (SOPInstanceUID) {
+      displaySet = displaySetService.getDisplaySetForSOPInstanceUID(
+        SOPInstanceUID,
+        SeriesInstanceUID
+      );
+    } else {
+      displaySet = displaySetService.getDisplaySetsForSeries(SeriesInstanceUID);
+    }
+
+    const { cachedStats } = data;
+
+    return {
+      uid: annotationUID,
+      SOPInstanceUID,
+      FrameOfReferenceUID,
+      // points,
+      metadata,
+      referenceSeriesUID: SeriesInstanceUID,
+      referenceStudyUID: StudyInstanceUID,
+      toolName: metadata.toolName,
+      displaySetInstanceUID: displaySet.displaySetInstanceUID,
+      label: metadata.label,
+      // displayText: displayText,
+      data: data.cachedStats,
+      type: 'CircleROIStartEndThreshold',
+      // getReport,
+    };
+  },
+};
+
+export default CircleROIStartEndThreshold;

extensions/tmtv/src/utils/measurementServiceMappings/RectangleROIStartEndThreshold.js

@@ -0,0 +1,63 @@
+import SUPPORTED_TOOLS from './constants/supportedTools';
+import { getSOPInstanceAttributes } from '@ohif/extension-cornerstone';
+
+const RectangleROIStartEndThreshold = {
+  toAnnotation: (measurement, definition) => {},
+
+  /**
+   * Maps cornerstone annotation event data to measurement service format.
+   *
+   * @param {Object} cornerstone Cornerstone event data
+   * @return {Measurement} Measurement instance
+   */
+  toMeasurement: (csToolsEventDetail, displaySetService, cornerstoneViewportService) => {
+    const { annotation, viewportId } = csToolsEventDetail;
+    const { metadata, data, annotationUID } = annotation;
+
+    if (!metadata || !data) {
+      console.warn('Length tool: Missing metadata or data');
+      return null;
+    }
+
+    const { toolName, referencedImageId, FrameOfReferenceUID } = metadata;
+    const validToolType = SUPPORTED_TOOLS.includes(toolName);
+
+    if (!validToolType) {
+      throw new Error('Tool not supported');
+    }
+
+    const { SOPInstanceUID, SeriesInstanceUID, StudyInstanceUID } = getSOPInstanceAttributes(
+      referencedImageId,
+      cornerstoneViewportService,
+      viewportId
+    );
+
+    let displaySet;
+
+    if (SOPInstanceUID) {
+      displaySet = displaySetService.getDisplaySetForSOPInstanceUID(
+        SOPInstanceUID,
+        SeriesInstanceUID
+      );
+    } else {
+      displaySet = displaySetService.getDisplaySetsForSeries(SeriesInstanceUID);
+    }
+
+    return {
+      uid: annotationUID,
+      SOPInstanceUID,
+      FrameOfReferenceUID,
+      // points,
+      metadata,
+      referenceSeriesUID: SeriesInstanceUID,
+      referenceStudyUID: StudyInstanceUID,
+      toolName: metadata.toolName,
+      displaySetInstanceUID: displaySet.displaySetInstanceUID,
+      label: metadata.label,
+      data: data.cachedStats,
+      type: 'RectangleROIStartEndThreshold',
+    };
+  },
+};
+
+export default RectangleROIStartEndThreshold;

extensions/tmtv/src/utils/measurementServiceMappings/constants/supportedTools.js

@@ -0,0 +1 @@
+export default ['RectangleROIStartEndThreshold'];

extensions/tmtv/src/utils/measurementServiceMappings/measurementServiceMappingsFactory.js

@@ -0,0 +1,41 @@
+import RectangleROIStartEndThreshold from './RectangleROIStartEndThreshold';
+import CircleROIStartEndThreshold from './CircleROIStartEndThreshold';
+
+const measurementServiceMappingsFactory = (
+  measurementService,
+  displaySetService,
+  cornerstoneViewportService
+) => {
+  return {
+    RectangleROIStartEndThreshold: {
+      toAnnotation: RectangleROIStartEndThreshold.toAnnotation,
+      toMeasurement: csToolsAnnotation =>
+        RectangleROIStartEndThreshold.toMeasurement(
+          csToolsAnnotation,
+          displaySetService,
+          cornerstoneViewportService
+        ),
+      matchingCriteria: [
+        {
+          valueType: measurementService.VALUE_TYPES.ROI_THRESHOLD_MANUAL,
+        },
+      ],
+    },
+    CircleROIStartEndThreshold: {
+      toAnnotation: CircleROIStartEndThreshold.toAnnotation,
+      toMeasurement: csToolsAnnotation =>
+        CircleROIStartEndThreshold.toMeasurement(
+          csToolsAnnotation,
+          displaySetService,
+          cornerstoneViewportService
+        ),
+      matchingCriteria: [
+        {
+          valueType: measurementService.VALUE_TYPES.ROI_THRESHOLD_MANUAL,
+        },
+      ],
+    },
+  };
+};
+
+export default measurementServiceMappingsFactory;