2b:null 2c:["$","title",null,{"children":"Fsaverage in FreeSurfer | Chuncheng | Observable"}] 31:T570,reColor = () => { // ["Normal", "Thickness", "Sulc", "Curv"] console.log("Recolor the cortex to", select); if (select === "Normal") { dynamicModel.rgbs = dynamicModel.normals; return "Normal: The cortex is colored with the cells' direction"; } if (select === "Thickness") { const colors = mkColors(cortexValues.thickness, colorMapStr); dynamicModel.rgbs = colors.rgbs; return "Thickness: The Thickness of the area, extent: " + colors.minMax; } if (select === "Curv") { const colors = mkColors(cortexValues.curv, colorMapStr); dynamicModel.rgbs = colors.rgbs; return ( "Thickness: The Curv structure of the area, extent: " + colors.minMax ); } if (select === "Sulc") { const colors = mkColors(cortexValues.sulc, colorMapStr); dynamicModel.rgbs = colors.rgbs; return ( "Thickness: The Sulc structure of the area, extent: " + colors.minMax ); } if (select == "Zstat") { const colors = mkColors(cortexValues.sulc, "interpolateGreys", "----"); const newColors = addColors( activites.values[selectZstatName], colorMapStr, colors.rgbs, 0.5 ); dynamicModel.rgbs = newColors.rgbs; return ( "Zstat: The zstat values of " + selectZstatName + ", extent: " + newColors.minMax ); } console.warn("Failed recolor the cortex to", select); 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2f:{"id":"e5d9accda7d84087","slug":"fsaverage-in-freesurfer","title":"Fsaverage in FreeSurfer","thumbnail":"2b7b33bfbef653810dff2fa847f9fffa2c8409c770270acb30e1ece5f244892e","access_level":"public","create_time":"$D2021-12-06T07:58:19.807Z","update_time":"$D2021-12-07T04:33:52.378Z","view_time":null,"first_public_time":"$D2021-12-06T09:05:06.185Z","fork":{"id":"100ec286f5a46dad","slug":"free-surfer-cortex-v2","title":"Free Surfer Cortex V2","owner":{"id":"bcd65cef1cb4d2ed","login":"listenzcc","name":"Chuncheng"}},"stars":0,"starred":false,"owner":{"type":"team","id":"bcd65cef1cb4d2ed","login":"listenzcc","name":"Chuncheng","avatar_url":"https://avatars-next.observableusercontent.com/bb3c68e77a708a587ffc2d663bb83421f20d67991dbe6c1623c6e5d2fb73d15e","tier":"starter_2024"},"version":1338,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"16328058352682a8","login":"listenzcc","name":"Chuncheng","avatar_url":"https://avatars-next.observableusercontent.com/bb3c68e77a708a587ffc2d663bb83421f20d67991dbe6c1623c6e5d2fb73d15e","tier":null}],"members":[{"type":"individual","id":"16328058352682a8","login":"listenzcc","name":"Chuncheng","avatar_url":"https://avatars-next.observableusercontent.com/bb3c68e77a708a587ffc2d663bb83421f20d67991dbe6c1623c6e5d2fb73d15e","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"title":"Fsaverage in FreeSurfer","cells":[{"id":0,"value":"# Fsaverage in FreeSurfer\n\n

[Docs](http://regl.party/api) | [Examples](https://regl-project.github.io/regl/www/gallery.html)

\n\nThe project displays the cortex surface of the [freesurfer toolbox](https://surfer.nmr.mgh.harvard.edu/).\n\n## User Operations\n\nIt is an interactive 3D scene,\nwhich allows user to operate and display on its own purpose\n\n- **Click and drag** to rotate the cortex;\n- **Scroll** to zoom;\n- **Drag** the scaler to bloom the surface;\n- **Select** the color base to change the color base.\n\nIt may slow on startup depending on your computer, please be patient.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":515,"value":"viewof scaler = Inputs.range([0, 1], { label: \"Scaler\", value: 0.5, step: 0.01 })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":810,"value":"viewof select = Inputs.select(\n [\"Normal\", \"Thickness\", \"Sulc\", \"Curv\", \"Zstat\"],\n {\n label: \"Select Color Base\",\n value: \"Thickness\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1320,"value":"viewof selectZstatName = Inputs.select(activites.names, {\n label: \"Select Zstat Name\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1191,"value":"viewof colorMapStr = Inputs.select(\n [\n \"interpolateGreys\",\n \"interpolateTurbo\",\n \"interpolateInferno\",\n \"interpolateCividis\",\n \"interpolateViridis\",\n \"interpolateMagma\",\n \"interpolateWarm\",\n \"interpolateYlGnBu\"\n ],\n {\n label: \"Color Map\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1221,"value":"viewof reverseColorMap = Inputs.checkbox([\"Reverse\"], {\n label: \"Reverse Color Map\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":879,"value":"{\n select;\n colorMapStr;\n reverseColorMap;\n selectZstatName;\n // reDraw();\n\n captionContext[0] = reColor();\n\n const fig = html`\n

\n ${canvas}\n

${captionContext[0]}

\n `;\n\n fig.value = canvas.value;\n return fig;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":929,"value":"captionContext = [\"Click the Blue Window to Start!!!\"]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":886,"value":"html`\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":539,"value":"cameraLst = () => {\n let cameraParams = Object.assign({\n center: [0, 3.5, 0],\n theta: (3.0 * Math.PI) / 4.0,\n phi: Math.PI / 15.0,\n distance: 300.0,\n damping: 0,\n noScroll: true,\n renderOnDirty: true\n });\n\n const camera = reglCamera(regl, cameraParams);\n return [camera];\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":578,"value":"camera = cameraLst()[0];","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":569,"value":"// Continuously updates\nregl.frame(() => {\n camera(function (state) {\n if (!state.dirty) return;\n\n regl.clear({ color: [0, 0.1, 0.26, 1] });\n\n drawModel(dynamicModel);\n });\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":542,"value":"// Scale by input\n{\n scaler;\n select;\n colorMapStr;\n selectZstatName;\n reDraw();\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":960,"value":"reDraw = () => {\n captionContext[0] = reColor();\n cameraLst()[0](function (state) {\n if (!state.dirty) return;\n\n regl.clear({ color: [0, 0.1, 0.26, 1] });\n\n let s = 0,\n model1 = 0,\n model2 = 0;\n\n if (scaler <= 0.5) {\n s = scaler * 2;\n model1 = lhPialModel;\n model2 = lhInflatedModel;\n } else {\n s = (scaler - 0.5) * 2;\n model1 = lhInflatedModel;\n model2 = lhSphereModel;\n }\n\n // Scale the Models\n // s==0: model1;\n // s==1: model2.\n for (let i = 0; i < lhPialModel.positions.length; i++) {\n for (let j = 0; j < 3; j++) {\n dynamicModel.positions[i][j] =\n (model2.positions[i][j] - model1.positions[i][j]) * s +\n model1.positions[i][j];\n }\n }\n\n drawModel(dynamicModel);\n });\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":551,"value":"drawModel = regl({\n frag: `\n #extension GL_OES_standard_derivatives : enable\n precision mediump float;\n varying vec3 vrgb;\n\n void main () {\n gl_FragColor = vec4(abs(vrgb), 0.8);\n }`,\n vert: `\n precision mediump float;\n uniform mat4 projection, view;\n attribute vec3 position, rgb;\n varying vec3 vrgb;\n\n void main () {\n vrgb = rgb;\n gl_Position = projection * view * vec4(position, 1.0);\n }`,\n attributes: {\n position: regl.prop(\"positions\"),\n rgb: regl.prop(\"rgbs\")\n },\n elements: regl.prop(\"cells\"),\n depth: {\n enable: true\n },\n blend: {\n enable: false,\n func: {\n srcRGB: \"src alpha\",\n srcAlpha: 1,\n dstRGB: \"one minus src alpha\",\n dstAlpha: 1\n },\n equation: {\n rgb: \"add\",\n alpha: \"add\"\n }\n }\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":751,"value":"$31","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1160,"value":"mkColors = (arr, _colorMapStr, reverseOption = reverseColorMap[0]) => {\n const colorMap = eval(`d3.${_colorMapStr}`);\n const extent = d3.extent(arr);\n\n let range = [0.1, 0.9];\n if (reverseOption === \"Reverse\") range = [0.9, 0.1];\n\n const scaler = d3.scaleLinear().domain(extent).range(range);\n\n const rgbs = new Array(arr.length);\n for (let i = 0; i < arr.length; i++) {\n const s = scaler(arr[i]);\n const rgb = d3.rgb(colorMap(s));\n rgbs[i] = [rgb.r / 255, rgb.g / 255, rgb.b / 255];\n }\n\n const minMax = extent[0] + \" -- \" + extent[1];\n return { rgbs, minMax };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1264,"value":"addColors = (arr, _colorMapStr, rgbs, threshold) => {\n const colorMap = eval(`d3.${_colorMapStr}`);\n const extent = d3.extent(arr);\n\n let range = [0.1, 0.9];\n if (reverseColorMap[0] === \"Reverse\") range = [0.9, 0.1];\n\n const scaler = d3.scaleLinear().domain(extent).range(range);\n\n for (let i = 0; i < rgbs.length; i++) {\n if (math.abs(arr[i]) < threshold) continue;\n const s = scaler(arr[i]);\n\n const rgb = d3.rgb(colorMap(s));\n rgbs[i] = [rgb.r / 255, rgb.g / 255, rgb.b / 255];\n }\n\n const minMax = extent[0] + \" -- \" + extent[1];\n return { rgbs, minMax };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":496,"value":"## OBJ Data","pinned":true,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":555,"value":"dynamicModel = mkModel(lhPial)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":485,"value":"lhSphereModel = mkModel(lhSphere)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":490,"value":"lhPialModel = mkModel(lhPial)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":494,"value":"lhInflatedModel = mkModel(lhInflated)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1156,"value":"cortexValues = {\n const _thickness = await FileAttachment(\"lh-thickness.values.csv\").csv();\n const _sulc = await FileAttachment(\"lh-sulc.values.csv\").csv();\n const _curv = await FileAttachment(\"lh-curv.values.csv\").csv();\n const thickness = _thickness.map((e) => parseFloat(e[0]));\n const sulc = _sulc.map((e) => parseFloat(e[0]));\n const curv = _curv.map((e) => parseFloat(e[0]));\n return { thickness, sulc, curv };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1101,"value":"lhSphere = {\n const positions = await FileAttachment(\"lh-sphere.positions.csv\").csv();\n const cells = await FileAttachment(\"lh-sphere.cells.csv\").csv();\n return { positions, cells };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":465,"value":"lhPial = {\n const positions = await FileAttachment(\"lh-pial.positions.csv\").csv();\n const cells = await FileAttachment(\"lh-pial.cells.csv\").csv();\n return { positions, cells };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":469,"value":"lhInflated = {\n const positions = await FileAttachment(\"lh-inflated.positions.csv\").csv();\n const cells = await FileAttachment(\"lh-inflated.cells.csv\").csv();\n return { positions, cells };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1305,"value":"activites = {\n const names = [];\n const values = Object.create({});\n for (let e in fetchedData[0]) {\n if (e) {\n names.push(e);\n values[e] = [];\n }\n }\n\n for (let i = 0; i < fetchedData.length; i++) {\n for (let j = 0; j < names.length; j++) {\n values[names[j]].push(parseFloat(fetchedData[i][names[j]]));\n }\n }\n return { names, values };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1301,"value":"viewof table = Inputs.table(fetchedData, {})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1298,"value":"fetchedData = await FileAttachment(\"fetched_data.csv\").csv()","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1244,"value":"zstats = {\n const raw = await FileAttachment(\"zstat4.nii.gz.csv\").csv();\n const arr = [];\n // This explains how to align .nii.gz matrix into the vertex array\n for (let j = 0; j < 83; j++) {\n for (let i = 0; i < 1974; i++) {\n arr.push(1.0 * raw[i][j]);\n }\n }\n return arr;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":670,"value":"## Toolbox","pinned":true,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":1104,"value":"mkModel = (obj) => {\n const _positions = obj.positions,\n _cells = obj.cells;\n // const { _positions, _cells } = obj;\n const positions = _positions.map((e) => {\n return [e[0], e[1], e[2]].map(parseFloat);\n });\n const cells = _cells.map((e) => {\n return [0 + e[0], 0 + e[1], 0 + e[2]].map((e) => e - 0);\n });\n\n const normals = angleNormals(cells, positions);\n\n const rgbs = normals;\n\n return { positions, cells, normals, rgbs };\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":327,"value":"angleNormals = (await import(\"https://cdn.skypack.dev/angle-normals@1.0.0\"))\n .default","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":722,"value":"d3 = require(\"d3\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":683,"value":"math = require(\"mathjs\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":340,"value":"reglCamera = (await import(\"https://cdn.skypack.dev/regl-camera@2.1.1\")).default","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":422,"value":"regl = (await require(\"regl\"))({\n canvas: canvas,\n pixelRatio: 2,\n extensions: [\"oes_standard_derivatives\", \"OES_element_index_uint\"]\n})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":264,"value":"canvas = DOM.canvas(width, 500)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W32","stdlib":"1","titling":"auto"}} 30:"$2f:body"