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_config.js
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_config.js
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var papaya = papaya || {};
papaya.data = papaya.data || {};
papaya.data.Atlas = papaya.data.Atlas || {};
let core_data = "core_data"
papaya.data.configureAtlas = async function (viewer) {
console.log('configureAtlas')
if (this.atlas === null) {
return;
}
let boundaryData = viewer.atlas.boundaryData;
let boundaryVolumes = [];
for (let key in papaya.data.Atlases) {
try {
if (papaya.data.Atlases.hasOwnProperty(key)) {
let volume = papaya.data.Atlases[key].atlas.boundaryData.volume;
if (volume && volume !== boundaryData.volume) {
boundaryVolumes.push(volume);
}
}
} catch (err) {
// Unable to get volume, cannot be open
}
}
let loadVolume = (viewer.container.preferences.showVolumeBoundaries === "Yes");
let ctr = 0;
while (ctr < viewer.screenVolumes.length) {
// Unload current boundary if desired
if (viewer.screenVolumes[ctr].volume === boundaryData.volume) {
if (!loadVolume) {
viewer.closeOverlay(ctr);
break;
}
loadVolume = false;
}
// Unloaded other boundary files
for (let ctr2 = 0; ctr2 < boundaryVolumes.length; ctr2++) {
if (viewer.screenVolumes[ctr].volume === boundaryVolumes[ctr2]) {
viewer.closeOverlay(ctr);
break;
}
}
ctr++;
}
// Load the required image boundary
if (loadVolume) {
if (boundaryData.volume && viewer.loadingVolume === null) {
viewer.loadingVolume = boundaryData.volume;
viewer.initializeOverlay();
} else {
viewer.loadOverlay([viewer.container.findLoadableImage(boundaryData.boundaryimagefile, false).url],
true, false, false);
boundaryData.volume = viewer.loadingVolume;
}
}
// Load surface boundary data if not loaded
if (boundaryData && boundaryData.data == null) {
let result = viewer.container.findLoadableImage(boundaryData.boundarysurfacefile, false);
if (result.url) {
let data = await loadatlas(result.url, boundaryData);
let gii = gifti.parse(data);
if (gii.getZScoresDataArray()) {
boundaryData.data = gii.getZScoresDataArray().getData();
boundaryData.range.min = Math.min(...boundaryData.data);
boundaryData.range.max = Math.max(...boundaryData.data);
}
}
}
// Display the surface boundaries
if (viewer.surfaces.length > 0) {
let surface = viewer.surfaces[0];
boundaryData = (boundaryData && viewer.container.preferences.showSurfaceBoundaries === "Yes") ? boundaryData : null;
if (boundaryData !== surface.boundaryData) {
surface.boundaryData = boundaryData;
surface.generateColorData();
viewer.drawViewer();
}
}
drawColor2Surface()
}
function loadatlas(url, boundaryData) {
return new Promise(function (resolve, reject) {
let xhr = new XMLHttpRequest();
xhr.open('GET', url);
xhr.onload = function () {
if (this.status >= 200 && this.status < 300) {
resolve(xhr.response);
} else {
reject({
status: this.status,
statusText: xhr.statusText
});
}
};
xhr.onerror = function () {
reject({
status: this.status,
statusText: xhr.statusText
});
};
xhr.send();
});
}
PAPAYA_BUILD_NUM = "1594";
("use strict");
papaya.data.Atlas.boundaryData = papaya.data.Atlas.boundaryData || {}
var binaryMapper = binaryMapper || {}
papaya.data.Atlases = papaya.data.Atlases || {};
papaya.data.Atlases["vPaxinos"] = {
labels: {
atlas: {
data: {
label: [
{ index: 0, content: ": :background:" },
{ index: 1, content: ": :A1/A2 : areas 1 and 2 of cortex" },
{ index: 2, content: ": :A10 : area 10 of cortex" },
{ index: 3, content: ": :A11 : area 11 of cortex" },
{ index: 4, content: ": :A13L : area 13 of cortex lateral part" },
{ index: 5, content: ": :A13M : area 13 of cortex medial part" },
{ index: 6, content: ": :A13a : area 13a of cortex" },
{ index: 7, content: ": :A13b : area 13b of cortex" },
{ index: 8, content: ": :A14C : area 14 of cortex caudal part" },
{ index: 9, content: ": :A14R : area 14 of cortex rostral part" },
{
index: 10,
content: ": :A19DI : area 19 of cortex dorsointermediate part",
},
{ index: 11, content: ": :A19M : area 19 of cortex medial part" },
{ index: 12, content: ": :A23V : area 23 of cortex ventral part" },
{ index: 13, content: ": :A23a : area 23a of cortex" },
{ index: 14, content: ": :A23b : area 23b of cortex" },
{ index: 15, content: ": :A23c : area 23c of cortex" },
{ index: 16, content: ": :A24a : area 24a of cortex" },
{ index: 17, content: ": :A24b : area 24b of cortex" },
{ index: 18, content: ": :A24c : area 24c of cortex" },
{ index: 19, content: ": :A24d : area 24d of cortex" },
{ index: 20, content: ": :A25 : area 25 of cortex" },
{ index: 21, content: ": :A29a-c : area 29a-c of cortex" },
{ index: 22, content: ": :A29d : area 29d of cortex" },
{ index: 23, content: ": :A30 : area 30 of cortex" },
{ index: 24, content: ": :A31 : area 31 of cortex" },
{ index: 25, content: ": :A32 : area 32 of cortex" },
{ index: 26, content: ": :A32V : area 32 of cortex ventral part" },
{ index: 27, content: ": :A35 : area 35 of cortex" },
{ index: 28, content: ": :A36 : area 36 of cortex" },
{ index: 29, content: ": :A3a : area 3a of cortex (somatosensory)" },
{ index: 30, content: ": :A3b : area 3b of cortex (somatosensory)" },
{ index: 31, content: ": :A45 : area 45 of cortex" },
{ index: 32, content: ": :A46D : area 46 of cortex dorsal part" },
{ index: 33, content: ": :A46V : area 46 of cortex ventral part" },
{
index: 34,
content: ": :A47L : area 47 (old 12) of cortex lateral part",
},
{
index: 35,
content: ": :A47M : area 47 (old 12) of cortex medial part",
},
{
index: 36,
content: ": :A47O : area 47 (old 12) of cortex orbital part",
},
{
index: 37,
content: ": :A4ab : area 4 of cortex parts a and b (primary motor)",
},
{
index: 38,
content: ": :A4c : area 4 of cortex part c (primary motor)",
},
{ index: 39, content: ": :A6DC : area 6 of cortex dorsocaudal part" },
{ index: 40, content: ": :A6DR : area 6 of cortex dorsorostral part" },
{
index: 41,
content:
": :A6M : area 6 of cortex medial (supplementary motor) part",
},
{ index: 42, content: ": :A6Va : area 6 of cortex ventral part a" },
{ index: 43, content: ": :A6Vb : area 6 of cortex ventral part b" },
{ index: 44, content: ": :A8C : area 8 of cortex caudal part" },
{ index: 45, content: ": :A8aD : area 8a of cortex dorsal part" },
{ index: 46, content: ": :A8Av : area 8a of cortex ventral par" },
{ index: 47, content: ": :A8b : area 8b of cortex" },
{ index: 48, content: ": :A9 : area 9 of cortex" },
{ index: 49, content: ": :n.a. : dummy ROI" },
{ index: 50, content: ": :AI : agranular insular cortex" },
{
index: 51,
content: ": :AIP : anterior intraparietal area of cortex",
},
{ index: 52, content: ": :Apri : amygdalopiriform transition area" },
{ index: 53, content: ": :n.a. : dummy ROI" },
{ index: 54, content: ": :AuA1 : auditory cortex primary area" },
{ index: 55, content: ": :AuAL : auditory cortex anterolateral area" },
{ index: 56, content: ": :AuCL : auditory cortex caudolateral area" },
{ index: 57, content: ": :AuCM : auditory cortex caudomedial area" },
{
index: 58,
content: ": :AuCPB : auditory cortex caudal parabelt area",
},
{ index: 59, content: ": :AuML : auditory cortex middle lateral area" },
{ index: 60, content: ": :AuR : auditory cortex rostral area" },
{ index: 61, content: ": :AuRM : auditory cortex rostromedial area" },
{ index: 62, content: ": :AuRPB : auditory cortex rostral parabelt" },
{ index: 63, content: ": :AuRT : auditory cortex rostrotemporal" },
{
index: 64,
content: ": :AuRTL : auditory cortex rostrotemporal lateral area",
},
{
index: 65,
content: ": :AuRTM : auditory cortex rostrotemporal medial area",
},
{ index: 66, content: ": :n.a. : dummy ROI" },
{ index: 67, content: ": :DI : dysgranular insular cortex" },
{ index: 68, content: ": :n.a. : dummy ROI" },
{ index: 69, content: ": :n.a. : dummy ROI" },
{ index: 70, content: ": :Ent : entorhinal cortex" },
{
index: 71,
content: ": :FST : fundus of superior temporal sulcus area of cortex",
},
{ index: 72, content: ": :GI : granular insular cortex" },
{ index: 73, content: ": :Gu : gustatory cortex" },
{ index: 74, content: ": :n.a. : dummy ROI" },
{ index: 75, content: ": :Ipro : insular proisocortex" },
{ index: 76, content: ": :LIP : lateral intraparietal area of cortex" },
{ index: 77, content: ": :n.a. : dummy ROI" },
{ index: 78, content: ": :n.a. : dummy ROI" },
{ index: 79, content: ": :MIP : medial intraparietal area of cortex" },
{ index: 80, content: ": :n.a. : dummy ROI" },
{
index: 81,
content: ": :MST : medial superior temporal area of cortex",
},
{ index: 82, content: ": :n.a. : dummy ROI" },
{ index: 83, content: ": :OPAl : orbital periallocortex" },
{ index: 84, content: ": :OPro : orbital proisocortex" },
{
index: 85,
content: ": :OPt : occipito-parietal transitional area of cortex",
},
{ index: 86, content: ": :n.a. : dummy ROI" },
{ index: 87, content: ": :PE : parietal area PE" },
{ index: 88, content: ": :PEC : parietal area PE caudal part" },
{ index: 89, content: ": :PF : parietal area PF (cortex)" },
{ index: 90, content: ": :PFG : parietal area PFG (cortex)" },
{ index: 91, content: ": :PG : parietal area PG" },
{
index: 92,
content: ": :PGM : parietal area PG medial part (cortex)",
},
{
index: 93,
content:
": :IPa : parietal areas PGa and IPa (fundus of superior temporal ventral area) PGa -",
},
{ index: 94, content: ": :n.a. : dummy ROI" },
{ index: 95, content: ": :n.a. : dummy ROI" },
{ index: 96, content: ": :PaIL : parainsular cortex lateral part" },
{ index: 97, content: ": :PaIM : parainsular cortex medial part" },
{ index: 98, content: ": :n.a. : dummy ROI" },
{ index: 99, content: ": :n.a. : dummy ROI" },
{ index: 100, content: ": :Pir : piriform cortex" },
{ index: 101, content: ": :n.a. : dummy ROI" },
{ index: 102, content: ": :n.a. : dummy ROI" },
{
index: 103,
content:
": :ProM : proisocortical motor region (precentral opercular cortex)",
},
{ index: 104, content: ": :ProSt : prostriate area" },
{ index: 105, content: ": :ReI : retroinsular area (cortex)" },
{
index: 106,
content: ": :S2E : secondary somatosensory cortex external part",
},
{
index: 107,
content: ": :S2I : secondary somatosensory cortex internal part",
},
{
index: 108,
content:
": :S2PR : secondary somatosensory cortex parietal rostral area",
},
{
index: 109,
content:
": :S2PV : secondary somatosensory cortex parietal ventral area",
},
{ index: 110, content: ": :n.a. : dummy ROI" },
{
index: 111,
content: ": :STR : superior temporal rostral area (cortex)",
},
{
index: 112,
content: ": :TE1 : temporal area TE1 (inferior temporal cortex)",
},
{
index: 113,
content: ": :TE2 : temporal area TE2 (inferior temporal cortex)",
},
{
index: 114,
content: ": :TE3 : temporal area TE3 (inferior temporal cortex)",
},
{ index: 115, content: ": :TEO : temporal area TE occipital part" },
{ index: 116, content: ": :TF : temporal area TF" },
{ index: 117, content: ": :TFO : temporal area TF occipital part" },
{ index: 118, content: ": :TH : temporal area TH" },
{ index: 119, content: ": :TL : temporal area TL" },
{ index: 120, content: ": :TLO : temporal area TL occipital part" },
{
index: 121,
content:
": :TPO : temporo-parieto-occipital association area (superior temporal polysensory cortex)",
},
{ index: 122, content: ": :TPPro : temporopolar proisocortex" },
{ index: 123, content: ": :Tpro : temporal proisocortex" },
{ index: 124, content: ": :TPt : temporoparietal transitional area" },
{ index: 125, content: ": :n.a. : dummy ROI" },
{ index: 126, content: ": :V1 : primary visual cortex" },
{ index: 127, content: ": :V2 : visual area 2" },
{
index: 128,
content: ": :V3 : visual area 3 (ventrolateral posterior area)",
},
{ index: 129, content: ": :V3A : visual area 3A (dorsoanterior area)" },
{
index: 130,
content: ": :V4 : visual area 4 (ventrolatereral anterior area)",
},
{
index: 131,
content:
": :V4T : visual area 4 transitional part (middle temporal crescent)",
},
{ index: 132, content: ": :V5 : visual area 5 (middle temporal area)" },
{ index: 133, content: ": :V6 : visual area 6 (dorsomedial area)" },
{
index: 134,
content: ": :V6A : visual area 6A (posterior parietal medial area)",
},
{
index: 135,
content: ": :VIP : ventral intraparietal area of cortex",
},
{ index: 136, content: ": :n.a. : dummy ROI" },
{ index: 137, content: ": :n.a. : dummy ROI" },
{ index: 138, content: ": :n.a. : dummy ROI" },
{ index: 139, content: ": :n.a. : dummy ROI" },
{ index: 151, content: "HipF" },
{ index: 152, content: "Amy" },
{ index: 153, content: "Thal" },
{ index: 154, content: "ZI" },
{ index: 155, content: "Sth" },
{ index: 156, content: "MGN" },
{ index: 157, content: "LGN" },
{ index: 158, content: "Cd" },
{ index: 159, content: "Pu" },
{ index: 160, content: "Acb" },
{ index: 161, content: "Cl" },
{ index: 162, content: "Hypo" },
{ index: 163, content: "Sep" },
{ index: 164, content: "GP" },
{ index: 165, content: "IC" },
{ index: 166, content: "SC" },
{ index: 167, content: "SNR" },
{ index: 168, content: "PAG" },
{ index: 169, content: "HB" },
{ index: 170, content: "CeB" },
{ index: 151, content: ": :HipF : Hippocampalformation" },
{ index: 152, content: ": :Amy : Amygdala" },
{ index: 153, content: ": :Thal : Thalamus" },
{ index: 154, content: ": :ZI : Zonaincerta" },
{ index: 155, content: ": :Sth : Subthalamus" },
{ index: 156, content: ": :MGN : Medialgeniculatenucleus" },
{ index: 157, content: ": :LGN : Lateralgeniculatenucleus" },
{ index: 158, content: ": :Cd : Caudate" },
{ index: 159, content: ": :Pu : Putamen" },
{ index: 160, content: ": :Acb : Acumbens" },
{ index: 161, content: ": :Cl : Claustrumandendopirformclaustrum" },
{ index: 162, content: ": :Hypo : Hypothalamus" },
{ index: 163, content: ": :Sep : Septum" },
{ index: 164, content: ": :GP : Globuspallidus" },
{ index: 165, content: ": :IC : Inferiorcolliculus" },
{ index: 166, content: ": :SC : Superiorcolliculus" },
{ index: 167, content: ": :SNR : Substantianigra" },
{ index: 168, content: ": :PAG : Periaqueductalgray" },
{ index: 169, content: ": :HB : habenularnuclei" },
{ index: 170, content: ": :CeB : Cerebellum" },
],
},
header: {
images: {
summaryimagefile: "atlas_MBM_cortex_vPaxinos_both_same"
},
name: "Atlas V3 cortex Paxinos",
type: "Label",
// images: {
// summaryimagefile: "atlas_MBM_cortex_vPaxinos_and_subcortical",
// },
// display: "*.*",
// name: "Paxinos Atlas",
// type: "Label"
},
version: 2,
},
},
boundaryData: {
mapper: binaryMapper,
range: {
min: 0,
max: 0,
alpha: 0.3
},
boundarysurfacefile: 'Paxinos Surface Boundaries',
data: null,
}
};
papaya.data.Atlases["v4"] = {
labels: {
atlas: {
data: {
label: [
{ index: 0, content: ": :background :" }, { index: 1, content: ": :1-ACC : anterior cingulate cortex" }, { index: 2, content: ": :2-MedV1 : medial primary visual and MT/MST" }, { index: 3, content: ": :3-HighVisC : high-level 3" }, { index: 4, content: ": :4-ACC : anterior cingulate cortex" }, { index: 5, content: ": :5-MedV1 : medial primary visual and MT/MST" }, { index: 6, content: ": :6-LatV1 : lateral primary visual and MT/MST" }, { index: 7, content: ": :7-MedV1 : medial primary visual and MT/MST" },
{ index: 8, content: ": :8-MedV1 : medial primary visual and MT/MST" }, { index: 9, content: ": :9-HighVisA : high-level 1" }, { index: 10, content: ": :10-DorSoma : dorsal somatomotor" }, { index: 11, content: ": :11-OFC : orbital frontal" }, { index: 12, content: ": :12-ACC : anterior cingulate cortex" }, { index: 13, content: ": :13-HighVisB : high-level 2" }, { index: 14, content: ": :14-MedV1 : medial primary visual and MT/MST" }, { index: 15, content: ": :15-LatV1 : lateral primary visual and MT/MST" }, { index: 16, content: ": :16-MedV1 : medial primary visual and MT/MST" },
{ index: 17, content: ": :17-MedV1 : medial primary visual and MT/MST" }, { index: 18, content: ": :18-FPN : frontoparietal-like network" }, { index: 19, content: ": :19-AudIns : auditory and insular cortex" }, { index: 20, content: ": :20-LatV1 : lateral primary visual and MT/MST" }, { index: 21, content: ": :21-FPN : frontoparietal-like network" }, { index: 22, content: ": :22-ParapHipp : the parahippocampus/temporal pole" }, { index: 23, content: ": :23-ParapHipp : the parahippocampus/temporal pole" }, { index: 24, content: ": :24-ParapHipp : the parahippocampus/temporal pole" },
{ index: 25, content: ": :25-HighVisB : high-level 2" }, { index: 26, content: ": :26-HighVisC : high-level 3" }, { index: 27, content: ": :27-ForPole : frontal pole" }, { index: 28, content: ": :28-DorSoma : dorsal somatomotor" }, { index: 29, content: ": :29-DorSoma : dorsal somatomotor" }, { index: 30, content: ": :30-FPN : frontoparietal-like network" }, { index: 31, content: ": :31-ForPole : frontal pole" }, { index: 32, content: ": :32-OFC : orbital frontal" }, { index: 33, content: ": :33-AudIns : auditory and insular cortex" }, { index: 34, content: ": :34-Premotor : premotor" },
{ index: 35, content: ": :35-FPN : frontoparietal-like network" }, { index: 36, content: ": :36-ParapHipp : the parahippocampus/temporal pole" }, { index: 37, content: ": :37-VenSoma : ventral somatomotor" }, { index: 38, content: ": :38-ForPole : frontal pole" }, { index: 39, content: ": :39-DorSoma : dorsal somatomotor" }, { index: 40, content: ": :40-DMN : default-mode-like network" }, { index: 41, content: ": :41-ParapHipp : the parahippocampus/temporal pole" }, { index: 42, content: ": :42-FPN : frontoparietal-like network" }, { index: 43, content: ": :43-MedV1 : medial primary visual and MT/MST" },
{ index: 44, content: ": :44-OFC : orbital frontal" }, { index: 45, content: ": :45-Premotor : premotor" }, { index: 46, content: ": :46-AudIns : auditory and insular cortex" }, { index: 47, content: ": :47-ForPole : frontal pole" }, { index: 48, content: ": :48-HighVisA : high-level 1" }, { index: 49, content: ": :49-HighVisB : high-level 2" }, { index: 50, content: ": :50-HighVisC : high-level 3" }, { index: 51, content: ": :51-HighVisC : high-level 3" }, { index: 52, content: ": :52-ParapHipp : the parahippocampus/temporal pole" }, { index: 53, content: ": :53-ParapHipp : the parahippocampus/temporal pole" },
{ index: 54, content: ": :54-ParapHipp : the parahippocampus/temporal pole" }, { index: 55, content: ": :55-HighVisB : high-level 2" }, { index: 56, content: ": :56-ParapHipp : the parahippocampus/temporal pole" }, { index: 57, content: ": :57-OFC : orbital frontal" }, { index: 58, content: ": :58-FPN : frontoparietal-like network" }, { index: 59, content: ": :59-AudIns : auditory and insular cortex" }, { index: 60, content: ": :60-OFC : orbital frontal" }, { index: 61, content: ": :61-VenSoma : ventral somatomotor" }, { index: 62, content: ": :62-DMN : default-mode-like network" },
{ index: 63, content: ": :63-AudIns : auditory and insular cortex" }, { index: 64, content: ": :64-VenSoma : ventral somatomotor" }, { index: 65, content: ": :65-MedV1 : medial primary visual and MT/MST" }, { index: 66, content: ": :66-Premotor : premotor" }, { index: 67, content: ": :67-FPN : frontoparietal-like network" }, { index: 68, content: ": :68-ParapHipp : the parahippocampus/temporal pole" }, { index: 69, content: ": :69-DMN : default-mode-like network" }, { index: 70, content: ": :70-LatV1 : lateral primary visual and MT/MST" }, {
index: 71,
content: ": :71-ACC : anterior cingulate cortex"
}, { index: 72, content: ": :72-Premotor : premotor" }, { index: 73, content: ": :73-FPN : frontoparietal-like network" }, { index: 74, content: ": :74-DMN : default-mode-like network" }, { index: 75, content: ": :75-DMN : default-mode-like network" }, { index: 76, content: ": :76-ACC : anterior cingulate cortex" }, { index: 77, content: ": :77-MedV1 : medial primary visual and MT/MST" }, { index: 78, content: ": :78-ParapHipp : the parahippocampus/temporal pole" }, { index: 79, content: ": :79-AudIns : auditory and insular cortex" },
{ index: 80, content: ": :80-MedV1 : medial primary visual and MT/MST" }, { index: 81, content: ": :81-HighVisC : high-level 3" }, { index: 82, content: ": :82-HighVisB : high-level 2" }, { index: 83, content: ": :83-AudIns : auditory and insular cortex" }, { index: 84, content: ": :84-MedV1 : medial primary visual and MT/MST" }, { index: 85, content: ": :85-HighVisB : high-level 2" }, { index: 86, content: ": :86-HighVisA : high-level 1" }, { index: 87, content: ": :87-DMN : default-mode-like network" }, { index: 88, content: ": :88-ACC : anterior cingulate cortex" },
{ index: 89, content: ": :89-DMN : default-mode-like network" }, { index: 90, content: ": :90-HighVisA : high-level 1" }, { index: 91, content: ": :91-OFC : orbital frontal" }, { index: 92, content: ": :92-DorSoma : dorsal somatomotor" }, { index: 93, content: ": :93-OFC : orbital frontal" }, { index: 94, content: ": :94-OFC : orbital frontal" }, { index: 95, content: ": :95-HighVisC : high-level 3" }, { index: 96, content: ": :96-HighVisA : high-level 1" }, { index: 151, content: ": :HipF : Hippocampalformation" }, { index: 152, content: ": :Amy : Amygdala" },
{ index: 153, content: ": :Thal : Thalamus" }, { index: 154, content: ": :ZI : Zonaincerta" }, { index: 155, content: ": :Sth : Subthalamus" }, { index: 156, content: ": :MGN : Medialgeniculatenucleus" }, { index: 157, content: ": :LGN : Lateralgeniculatenucleus" }, { index: 158, content: ": :Cd : Caudate" }, { index: 159, content: ": :Pu : Putamen" }, { index: 160, content: ": :Acb : Acumbens" }, { index: 161, content: ": :Cl : Claustrumandendopirformclaustrum" }, { index: 162, content: ": :Hypo : Hypothalamus" }, { index: 163, content: ": :Sep : Septum" }, {
index: 164,
content: ": :GP : Globuspallidus"
}, { index: 165, content: ": :IC : Inferiorcolliculus" }, { index: 166, content: ": :SC : Superiorcolliculus" }, { index: 167, content: ": :SNR : Substantianigra" }, { index: 168, content: ": :PAG : Periaqueductalgray" }, { index: 169, content: ": :HB : habenularnuclei" }, { index: 170, content: ": :CeB : Cerebellum" }
]
},
header: {
images: { summaryimagefile: "v4_atlas" },
name: "Atlas V4 cortex FC",
type: "Label"
},
version: 2
}
},
boundaryData: {
mapper: binaryMapper,
range: {
min: 0,
max: 96,
alpha: 0.3
},
boundarysurfacefile: 'v4_surface_boundaries',
data: null,
}
}
papaya.data.Atlases['vH'] = {
labels: {
atlas: {
data: {
label: [{ index: 0, content: ": :background :" }, { index: 1, content: ": :A10 : Area10" }, { index: 2, content: ": :A9 : Area9" }, { index: 3, content: ": :A46 : Area46" }, { index: 4, content: ": :8a : Area8a" }, { index: 5, content: ": :8b : Area8b" }, { index: 6, content: ": :A47L : Area47lateral" }, { index: 7, content: ": :A47M : Area47medial" }, { index: 8, content: ": :A45 : Area45" }, { index: 9, content: ": :ProM : Proisocorticalmotorregion(precentralopercularcortex)" }, { index: 10, content: ": :A32V : Area32ventral" },
{ index: 11, content: ": :A32D : Area32dorsal" }, { index: 12, content: ": :A14 : Area14" }, { index: 13, content: ": :A24a : Area24a" }, { index: 14, content: ": :A24b : Area24b" }, { index: 15, content: ": :A24cd : Area24cd" }, { index: 16, content: ": :A25 : Area25" }, { index: 17, content: ": :A11L : Area11lateral" }, { index: 18, content: ": :A11M : Area11medial" }, { index: 19, content: ": :A13L : Area13lateral" }, { index: 20, content: ": :A13M : Area13medial" }, { index: 21, content: ": :Gu : Gustatorycortex" }, { index: 22, content: ": :Opro : Orbitalproisocortex" },
{ index: 23, content: ": :OPAl : Orbitalpreiallocortex" }, { index: 24, content: ": :A6D : Area6dorsal" }, { index: 25, content: ": :A6M : Area6medial" }, { index: 26, content: ": :A6V : Areaventral" }, { index: 27, content: ": :A4M : Area4medal" }, { index: 28, content: ": :A4L : Area4lateral" }, { index: 29, content: ": :S1M : Primarysomatosensorymedial" }, { index: 30, content: ": :S1D : Primarysomatosensorydorsal" }, { index: 31, content: ": :S1V : Primarysomatosensoryventral" }, { index: 32, content: ": :S2a : Secondarysomatosensoryareaa" }, {
index: 33,
content: ": :S2b : Secondarysomatosensoryareab"
}, { index: 34, content: ": :Core : Auditorycorearea" }, { index: 35, content: ": :BeltM : Auditorybeltareamedial" }, { index: 36, content: ": :BeltL : Auditorybeltarealateral" }, { index: 37, content: ": :PBR : Auditoryparabeltarearostral" }, { index: 38, content: ": :PBC : Auditoryparabeltareacaudal" }, { index: 39, content: ": :STR : Superiortemporalrostralarea" }, { index: 40, content: ": :AI : Argranularinsularcortex" }, { index: 41, content: ": :DI : Dysgranularinsularcortex" }, { index: 42, content: ": :GI : Granularinsularcortex" },
{ index: 43, content: ": :ReI : Retroinsulararea" }, { index: 44, content: ": :PaIR : Parainsularcortexrostral" }, { index: 45, content: ": :PaIC : Parainsularcortexcaudal" }, { index: 46, content: ": :Tpt : Temporoparietaltransitionalarea" }, { index: 47, content: ": :TPOR : Temporo-parito-occipitalassociationarearostral" }, { index: 48, content: ": :TPOC : Temporo-parito-occipitalassociationareacaudal" }, { index: 49, content: ": :FSTR : Fundusofsuperiortemproalarearostral" }, { index: 50, content: ": :FSTC : Fundusofsuperiortemproalareacaudal" },
{ index: 51, content: ": :TEa : Interiortemporalareaa" }, { index: 52, content: ": :TEb : Interiortemporalareab" }, { index: 53, content: ": :TEc : Interiortemporalareac" }, { index: 54, content: ": :TEd : Interiortemporalaread" }, { index: 55, content: ": :TEe : Interiortemporalareae" }, { index: 56, content: ": :TEf : Interiortemporalareaf" }, { index: 57, content: ": :TPPro : Temporopolarproisocortex" }, { index: 58, content: ": :PrhR : Perihinalcortexrostral" }, { index: 59, content: ": :PrhC : Perihinalcortexcaudal" }, { index: 60, content: ": :Enta : Entorhinalcortexa" },
{ index: 61, content: ": :Entb : Entorhinalcortexb" }, { index: 62, content: ": :PHGa : Parahippocampalcomplexa" }, { index: 63, content: ": :PHGb : Parahippocampalcomplexb" }, { index: 64, content: ": :PHGc : Parahippocampalcomplexc" }, { index: 65, content: ": :Pri : Piriform" }, { index: 66, content: ": :SB : Subiculum" }, { index: 67, content: ": :PEa : ParietalareaPEa" }, { index: 68, content: ": :PEb : ParietalareaPEb" }, { index: 69, content: ": :PF/PFGa : ParietalareaPF/PFGa" }, { index: 70, content: ": :PF/PFGb : ParietalareaPF/PFGb" }, {
index: 71,
content: ": :PGa : ParietalareaPGa"
}, { index: 72, content: ": :PGb : ParietalareaPGa" }, { index: 73, content: ": :Opta : Occipito-parietaltranslationalareaa" }, { index: 74, content: ": :Optb : Occipito-parietaltranslationalareab" }, { index: 75, content: ": :IPa : Intraparietalareaa" }, { index: 76, content: ": :IPb : Intraparietalareab" }, { index: 77, content: ": :IPc : Intraparietalareac" }, { index: 78, content: ": :IPd : Intraparietalaread" }, { index: 79, content: ": :A23a : Area23a" }, { index: 80, content: ": :A23b : Area23b" }, { index: 81, content: ": :A23V : Area23ventral" },
{ index: 82, content: ": :A29M : Area29medial" }, { index: 83, content: ": :A30 : Area30" }, { index: 84, content: ": :A29V : Area29ventral" }, { index: 85, content: ": :A31 : Area31" }, { index: 86, content: ": :PGMa : Parietalareamediala" }, { index: 87, content: ": :PGMb : Parietalareamedialb" }, { index: 88, content: ": :ProSt : Prostriatearea" }, { index: 89, content: ": :V1a : VisualareaV1a" }, { index: 90, content: ": :V1b : VisualareaV1b" }, { index: 91, content: ": :V2M : VisualareaV2medial" }, { index: 92, content: ": :V2L : VisualareaV2lateral" }, {
index: 93,
content: ": :V2V : VisualareaV2ventral"
}, { index: 94, content: ": :V3D : VisualareaV3dorsal" }, { index: 95, content: ": :V3L : VisualareaV3lateral" }, { index: 96, content: ": :V3V : VisualareaV3ventral" }, { index: 97, content: ": :V4L : VisualareaV4lateral" }, { index: 98, content: ": :V4V : VisualareaV4ventral" }, { index: 99, content: ": :V5R : VisualareaV5rostral" }, { index: 100, content: ": :V5C : VisualareaV5caudal" }, { index: 101, content: ": :V6R : VisualareaV6rostral" }, { index: 102, content: ": :V6M : VisualareaV6medial" }, {
index: 103,
content: ": :V6D : VisualareaV6dorsal"
}, { index: 104, content: ": :A19DI : Area19dorsointermediatepart" }, { index: 105, content: ": :A19M : A19medialpart" }, { index: 106, content: ": :MST : Medialsuperiortemporalarea" }, { index: 151, content: ": :HipF : Hippocampalformation" }, { index: 152, content: ": :Amy : Amygdala" }, { index: 153, content: ": :Thal : Thalamus" }, { index: 154, content: ": :ZI : Zonaincerta" }, { index: 155, content: ": :Sth : Subthalamus" }, { index: 156, content: ": :MGN : Medialgeniculatenucleus" }, { index: 157, content: ": :LGN : Lateralgeniculatenucleus" },
{ index: 158, content: ": :Cd : Caudate" }, { index: 159, content: ": :Pu : Putamen" }, { index: 160, content: ": :Acb : Acumbens" }, { index: 161, content: ": :Cl : Claustrumandendopirformclaustrum" }, { index: 162, content: ": :Hypo : Hypothalamus" }, { index: 163, content: ": :Sep : Septum" }, { index: 164, content: ": :GP : Globuspallidus" }, { index: 165, content: ": :IC : Inferiorcolliculus" }, { index: 166, content: ": :SC : Superiorcolliculus" }, { index: 167, content: ": :SNR : Substantianigra" }, { index: 168, content: ": :PAG : Periaqueductalgray" },
{ index: 169, content: ": :HB : habenularnuclei" }, { index: 170, content: ": :CeB : Cerebellum" }]
},
header: {
images: { summaryimagefile: "vH_atlas" },
name: "Atlas V3 cortex vH",
type: "Label"
}, version: 2
}
},
boundaryData: {
mapper: function () { console.log(arguments) },
range: {
min: 0,
max: 0,
alpha: 0.3
},
boundarysurfacefile: 'vH_surface_boundaries',
data: null,
}
}
papaya.data.Atlases['vNetwork'] = {
labels: {
atlas: {
data: {
label: [
{ index: 1, content: "ventral somatomotor"},
{ index: 2, content: "dorsal somatomotor"},
{ index: 3, content: "frontal pole"},
{ index: 4, content: "the parahippocampus/temporal pole"},
{ index: 5, content: "orbital frontal"},
{ index: 6, content: "auditory and insular cortex (salience-related)"},
{ index: 7, content: "frontoparietal-like network"},
{ index: 8, content: "default-mode-like network"},
{ index: 9, content: "visual-related network: medial primary visual and MT/MST"},
{ index: 10, content: "visual-related network: lateral primary visual and MT/MST"},
{ index: 11, content: "visual-related network: high-level 1"},
{ index: 12, content: "visual-related network: high-level 2"},
{ index: 13, content: "visual-related network: high-level 3"},
{ index: 14, content: "anterior cingulate cortex (salience-related)"},
{ index: 15, content: "premotor"},
]
},
header: {
images: { summaryimagefile: "v4_network" },
name: "Atlas V4 networks parcellation",
type: "Label"
}, version: 2
}
},
boundaryData: {
mapper: binaryMapper,
range: {
min: 0,
max: 0,
alpha: 0.3
},
// boundaryimagefile: 'Paxinos Boundaries',
boundarysurfacefile: 'vNetwork_surface_boundaries',
data: null,
}
}
var papayaLoadableImages = [
{ //0
hide: true,
// name: "atlas_MBM_cortex_vPaxinos_both_same",
// nicename: "Atlas",
// url: "data/atlas_MBM_cortex_vPaxinos_both_same.nii.gz",
},
{ //1
name: "atlas_MBM_cortex_vPaxinos_both_same",
nicename: "atlas_MBM_cortex_vPaxinos_both_same",
url: "data/atlas_MBM_cortex_vPaxinos_right.nii.gz",
hide: true
},
{ //2
name: "template_myelinmap_brain",
nicename: "template_myelinmap",
url: "data/template_myelinmap_brain.nii.gz",
hide: false
},
{//3
name: "template_T1w_brain",
nicename: "template_T1w",
url: "data/template_T1w_brain.nii.gz",
hide: false
},
{ //4
name: "template_T2w_brain",
nicename: "template_T2w",
url: "data/template_T2w_brain.nii.gz",
hide: false
},
{ //5
name: 'graymid',
nicename: "Gray Mid Right",
url: "data" + "/surfFS.rh.graymid.surf.gii",
surface: true,
hide: true
},
{ //6
name: "Paxinos Surface Boundaries",
nicename: "Paxinos Surface Boundaries",
url: "data" + '/atlas_MBM_cortex_vPaxinos_and_subcortical_borders.R.func.gii',
surface: true,
hide: true
},
{ //7
name: 'Paxinos Boundaries',
nicename: "Paxinos Atlas Boundaries",
url: "data" + '/atlas_MBM_cortex_vPaxinos_and_subcortical_borders.nii.gz',
hide: true
},
{ //8
name: 'v4_atlas',
nicename: "v4_atlas",
url: "data" + '/atlas_MBMv4_cortex_parcellation_right.nii.gz',
hide: true
},
{ //9
name: 'vH_atlas',
nicename: "vH_atlas",
url: "data" + '/atlas_MBM_cortex_vH_right.nii.gz',
hide: true
},
{ //10
name: 'parcellation_primary',
nicename: "parcellation_primary",
url: "data" + '/atlas_MBMv4_networks_parcellation_primary.nii.gz',
hide: false
},
{ //11
name: 'parcellation_secondary',
nicename: "parcellation_secondary",
url: "data" + '/atlas_MBMv4_networks_parcellation_secondary.nii.gz',
hide: false
},
{ //12
name: 'v4 surface label',
nicename: "v4 surface label",
url: "data" + '/surfFS.rh.MBMv4_cortex_parcellation.label.gii',
surface: true,
},
{ //13
name: 'v4 surface shape',
nicename: "v4 surface shape",
url: "data" + '/surfFS.rh.MBMv4_cortex_parcellation.R.func.gii',
surface: true,
},
{ //14 network
name: 'v4_network',
nicename: "v4 network",
url: "data" + '/atlas_MBMv4_networks_parcellation.nii.gz',
},
{ // 15
name: 'vH_surface',
nicename: 'vH surface',
url: 'data' + '/surfFS.rh.MBM_cortex_vH_boundary.shape.gii'
},
// -----------------------------
{ // 16
name: 'v4_surface_boundaries',
// nicename: 'vH surface',
url: 'data' + '/GZipBase64Binary_surfFS3.rh.MBMv4_cortex_parcellation.boundary.func.gii'
},
{ // 17
name: 'vH_surface_boundaries',
// nicename: 'vH surface',
url: 'data' + '/GZipBase64Binary_surfFS.rh.MBM_cortex_vH_boundary.func.gii'
},
{ // 18
name: 'vNetwork_surface_boundaries',
// nicename: 'vH surface',
url: 'data' + '/GZipBase64Binary_surfFS.rh.MBMv4_networks_parcellation_primary_boundary.func.gii'
},
];
// 这边应该有一个判断 然后选择atlas的逻辑
let atlas = document.querySelector('.papaya').getAttribute('atlas')
papaya.data.Atlas = papaya.data.Atlases[atlas]
var params = [];
// params["surfaces"] = ['data/surfFS.rh.graymid.surf.gii','data/atlas_MBM_cortex_vH_skeleton.R.func.gii'];
// params["surfaces"] = ['otherData/surfFS.CERB.pial_shift.surf.gii']
// params["surfaces"] = ['newData/surfFS.CERB.flatmap.surf.gii']
params["surfaces"] = ['otherData/surfFS.CERB.pial_shifti.surf(1).gii']
// params["orthogonalTall"] = true;
// params["surfaces"] = ['data/group_44_61_27_Z.R.func.gii']
switch (atlas) {
case "vPaxinos":
params["images"] = ['otherData/Template_sym_MTR_80um_CERB_small.nii.gz', 'otherData/change_sub_all_gradient1.nii.gz'];
params["atlas"] = papayaLoadableImages[1].url;
break;
case "v4":
params["images"] = ['otherData/Template_sym_MTR_80um_CERB_small.nii.gz', 'otherData/change_sub_all_5k_8k_gradient1.nii.gz'];
params["atlas"] = papayaLoadableImages[8].url;
break;
case "vH":
params["images"] = ['data/template_myelinmap_brain.nii.gz', papayaLoadableImages[9].url];
params["atlas"] = papayaLoadableImages[9].url;
break;
case "vNetwork":
params["images"] = ['data/template_myelinmap_brain.nii.gz', papayaLoadableImages[14].url];
params["atlas"] = papayaLoadableImages[14].url;
default:
break;
}
params["radiological"] = true
params["luts"] = [
{
name: "Custom",
data: [
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/** 试一下把rgb归一化 */
// params['luts'][0].data = params['luts'][0].data.map(([pctg, r, g, b])=>{
// return [pctg, r/255,g/255,b/255]
// })
console.log(params['luts'])
document.onclick = (e)=>{
console.log(e)
params['luts'] = {
name: 'Custom2',
data: [[0, 1,0,1]]
}
}
params["atlas_MBM_cortex_vPaxinos_right.nii.gz"] = {
min: 0,
max: 259,
lut: "Custom",
};
params['atlas_MBMv4_cortex_parcellation_right.nii.gz'] = {
min: 0,
max: 259,
lut: "Custom",
};
params['atlas_MBM_cortex_vH_right.nii.gz'] = {
min: 0,
max: 259,
lut: "Custom",
};
params['atlas_MBMv4_networks_parcellation.nii.gz'] = {
min: 0,
max: 259,
lut: "Custom",
};
params['template_myelinmap_brain.nii.gz'] = {
min: 0,
max: 3
}
params['change_sub_all_gradient1.nii.gz'] = {
min:-0.1,
max:0.1,
lut: 'Custom1'
}
document.addEventListener('*', (e)=>{
console.log(e)
})
// window.onload = function() {
// const _finishedLoad = papaya.volume.Volume.prototype.finishedLoad
// const _this = papaya.volume.Volume.prototype
// papaya.volume.Volume.prototype.finishedLoad = ()=>{
// _finishedload()
// console.log('finished load')
// }
// }
const drawColor2Surface = () => {
const surface = papayaContainers[0].viewer.surfaces[0]
const viewer = papayaContainers[0].viewer
// 这里1
const volume = papayaContainers[0].viewer.screenVolumes[1].volume
console.log(surface, viewer,volume)
console.log(surface.parametricData)
// const surfaceDataUrl = 'otherData/sub_all_gradient1_group.func.gii'
const surfaceDataUrl = 'otherData/sub_all_5k_8k_gradient1_group.func.gii'
fetch(surfaceDataUrl, {
method: 'GET',
headers: {
'Content-Type': 'text/xml',
},
}).then(res=>res.text()).then(_data=>{
const data = gifti.parse(_data).getZScoresDataArray().getData()
surface.parametricData.push({
viewer: viewer,
volume: volume,
data: data,
})
viewer.drawViewer(!0)
console.log('done')
})
}