From 904dee52f4c79bd8c8ab386a20997b833d920487 Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Thu, 15 Apr 2021 17:21:44 +0200
Subject: [PATCH] hotfix: cleaned freesurfer
---
deploy/csp/index.js | 2 +-
src/index.html | 2 +-
src/res/ext/freesurfer.json | 53 ++++++++++++++++++-
.../threeSurferGlue/threeSurfer.component.ts | 6 ++-
4 files changed, 59 insertions(+), 4 deletions(-)
diff --git a/deploy/csp/index.js b/deploy/csp/index.js
index 23deb8495..ae946653b 100644
--- a/deploy/csp/index.js
+++ b/deploy/csp/index.js
@@ -120,7 +120,7 @@ module.exports = (app) => {
'unpkg.com/react@16/umd/', // plugin load external lib -> react
'unpkg.com/kg-dataset-previewer@1.2.0/', // preview component
'cdnjs.cloudflare.com/ajax/libs/mathjax/', // math jax
- 'https://unpkg.com/three-surfer@0.0.5/dist/bundle.js', // for threeSurfer (freesurfer support in browser)
+ 'https://unpkg.com/three-surfer@0.0.7/dist/bundle.js', // for threeSurfer (freesurfer support in browser)
(req, res) => res.locals.nonce ? `'nonce-${res.locals.nonce}'` : null,
...SCRIPT_SRC,
...WHITE_LIST_SRC,
diff --git a/src/index.html b/src/index.html
index a1df7bb26..aa495bad5 100644
--- a/src/index.html
+++ b/src/index.html
@@ -14,7 +14,7 @@
<script src="https://unpkg.com/kg-dataset-previewer@1.2.0/dist/kg-dataset-previewer/kg-dataset-previewer.js" defer>
</script>
- <script src="https://unpkg.com/three-surfer@0.0.5/dist/bundle.js" defer></script>
+ <script src="https://unpkg.com/three-surfer@0.0.7/dist/bundle.js" defer></script>
<title>Interactive Atlas Viewer</title>
<script type="application/ld+json">
diff --git a/src/res/ext/freesurfer.json b/src/res/ext/freesurfer.json
index 375f31574..a9bae8dd3 100644
--- a/src/res/ext/freesurfer.json
+++ b/src/res/ext/freesurfer.json
@@ -15,9 +15,60 @@
"label_bv_hcp32k_lh": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/julichbrain_labels/lh.JulichBrain_MPMAtlas_l_N10_nlin2Stdicbm152asym2009c_publicDOI_83fb39b2811305777db0eb80a0fc8b53.allSub_RF_ANTs_MNI152_orig_to_hcp32k.gii",
"label_bv_hcp32k_rh": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/julichbrain_labels/rh.JulichBrain_MPMAtlas_r_N10_nlin2Stdicbm152asym2009c_publicDOI_172e93a5bec140c111ac862268f0d046.allSub_RF_ANTs_MNI152_orig_to_hcp32k.gii",
"label_ants_hcp32k_lh": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/julichbrain_labels/lh.JulichBrain_MPMAtlas_l_N10_nlin2Stdicbm152asym2009c_publicDOI_83fb39b2811305777db0eb80a0fc8b53.BV_MNI152_orig_to_hcp32k.gii",
- "label_ants_hcp32k_rh": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/julichbrain_labels/rh.JulichBrain_MPMAtlas_r_N10_nlin2Stdicbm152asym2009c_publicDOI_172e93a5bec140c111ac862268f0d046.BV_MNI152_orig_to_hcp32k.gii"
+ "label_ants_hcp32k_rh": "https://neuroglancer.humanbrainproject.eu/precomputed/freesurfer/20210305/julichbrain_labels/rh.JulichBrain_MPMAtlas_r_N10_nlin2Stdicbm152asym2009c_publicDOI_172e93a5bec140c111ac862268f0d046.BV_MNI152_orig_to_hcp32k.gii",
+ "label_fsaverage6_cleaned_lh":"https://neuroglancer-dev.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/lh.JulichBrain_MPMAtlas_l_N10_nlin2Stdicbm152asym2009c_publicDOI_83fb39b2811305777db0eb80a0fc8b53.BV_MNI152_orig_to_fsaverage6_cleaned.gii",
+ "label_fsaverage_cleaned_lh":"https://neuroglancer-dev.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/lh.JulichBrain_MPMAtlas_l_N10_nlin2Stdicbm152asym2009c_publicDOI_83fb39b2811305777db0eb80a0fc8b53.BV_MNI152_orig_to_fsaverage_cleaned.gii",
+ "label_hcp32k_cleaned_lh":"https://neuroglancer-dev.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/lh.JulichBrain_MPMAtlas_l_N10_nlin2Stdicbm152asym2009c_publicDOI_83fb39b2811305777db0eb80a0fc8b53.BV_MNI152_orig_to_hcp32k_cleaned.gii",
+ "label_fsaverage6_cleaned_rh":"https://neuroglancer-dev.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/rh.JulichBrain_MPMAtlas_r_N10_nlin2Stdicbm152asym2009c_publicDOI_172e93a5bec140c111ac862268f0d046.BV_MNI152_orig_to_fsaverage6_cleaned.gii",
+ "label_fsaverage_cleaned_rh":"https://neuroglancer-dev.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/rh.JulichBrain_MPMAtlas_r_N10_nlin2Stdicbm152asym2009c_publicDOI_172e93a5bec140c111ac862268f0d046.BV_MNI152_orig_to_fsaverage_cleaned.gii",
+ "label_hcp32k_cleaned_rh":"https://neuroglancer-dev.humanbrainproject.eu/precomputed/data-repo/20210415-new-freesurfer/rh.JulichBrain_MPMAtlas_r_N10_nlin2Stdicbm152asym2009c_publicDOI_172e93a5bec140c111ac862268f0d046.BV_MNI152_orig_to_hcp32k_cleaned.gii"
},
"modes": [
+ {
+ "name": "cleaned/fsaverage6/pial",
+ "meshes": [
+ {
+ "mesh": "rootUrl:fsa_fsa6:/lh.pial.gii",
+ "colormap": "label_fsaverage6_cleaned_lh:",
+ "hemisphere": "left"
+ },
+ {
+ "mesh": "rootUrl:fsa_fsa6:/rh.pial.gii",
+ "colormap": "label_fsaverage6_cleaned_rh:",
+ "hemisphere": "right"
+ }
+ ]
+ },
+ {
+ "name": "cleaned/fsaverage/pial",
+ "meshes": [
+ {
+ "mesh": "rootUrl:fsa_fsa:/lh.pial.gii",
+ "colormap": "label_fsaverage_cleaned_lh:",
+ "hemisphere": "left"
+ },
+ {
+ "mesh": "rootUrl:fsa_fsa:/rh.pial.gii",
+ "colormap": "label_fsaverage_cleaned_rh:",
+ "hemisphere": "right"
+ }
+ ]
+ },
+ {
+ "name": "cleaned/hcp32k/pial",
+ "meshes": [
+ {
+ "mesh": "rootUrl:fsa_fsa:/lh.pial.gii",
+ "colormap": "label_hcp32k_cleaned_lh:",
+ "hemisphere": "left"
+ },
+ {
+ "mesh": "rootUrl:fsa_fsa:/rh.pial.gii",
+ "colormap": "label_hcp32k_cleaned_rh:",
+ "hemisphere": "right"
+ }
+ ]
+ },
{
"name": "fsaverage/fsaverage/pial",
"meshes": [
diff --git a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
index a77b837ca..b68770f66 100644
--- a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
+++ b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
@@ -68,7 +68,11 @@ export class ThreeSurferGlueCmp implements IViewer, OnChanges, AfterViewInit, On
const tsC = await this.tsRef.loadColormap(
parseContext(colormap, [this.config['@context']])
)
- const colorIdx = tsC[0].getData()
+
+ let colorIdx = tsC[0].getData()
+ if (tsC[0].attributes.DataType === 'NIFTI_TYPE_INT16') {
+ colorIdx = (window as any).ThreeSurfer.GiftiBase.castF32UInt16(colorIdx)
+ }
this.loadedMeshes.push({
threeSurfer: tsM,
--
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