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FSA

This is a Github repository contains code and instructions for calculating personalized Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia. Details of the method are described in the article:

A neuroimaging biomarker for striatal dysfunction in schizophrenia. Nat Med (2020). https://doi.org/10.1038/s41591-020-0793-8

Getting Started

  • FSA is currently developed based on Python 2.X, requiring Python packages scipy, nilearn, sklearn, and joblib.

  • Please download the essential materials (e.g. SVM model) from figshare.

  • The FSA is currently developed and validated using the resting-state MRI data preprocessed by a open-source tool BRANT. Briefly, the raw fMRI image was preprocessed by slice timing, realign, coregister, normalization and denoising. Our model was validated based on the preprocessed fMRI images with global signal regression ('fdGSRwra*') and normalized fALFF images ('fALFF_z_').

  • Once established prerequisites above, personalized FSA score can be easily calculated parallelly following instructions and code in fsa.ipynb.

When using BRANT, please cite:

Copyright Information

The materials and code to calculate personalized FSA score is available for noncommercial use and exclusively for research purpose. For potential commercial use, please contact Bing Liu at bing.liu@bnu.edu.cn.

About

Calculation of Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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FSA
This is a Github repository contains code and instructions for calculating personalized Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia. Details of the method are described in the article:
A neuroimaging biomarker for striatal dysfunction in schizophrenia. Nat Med (2020). https://doi.org/10.1038/s41591-020-0793-8
Getting Started
  • FSA is currently developed based on Python 2.X, requiring Python packages scipy, nilearn, sklearn, and joblib.
  • Please download the essential materials (e.g. SVM model) from figshare.
  • The FSA is currently developed and validated using the resting-state MRI data preprocessed by a open-source tool BRANT. Briefly, the raw fMRI image was preprocessed by slice timing, realign, coregister, normalization and denoising. Our model was validated based on the preprocessed fMRI images with global signal regression ('fdGSRwra*') and normalized fALFF images ('fALFF_z_').
  • Once established prerequisites above, personalized FSA score can be easily calculated parallelly following instructions and code in fsa.ipynb.
When using BRANT, please cite:
Copyright Information
The materials and code to calculate personalized FSA score is available for noncommercial use and exclusively for research purpose. For potential commercial use, please contact Bing Liu at bing.liu@bnu.edu.cn.
About
Calculation of Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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FSA
This is a Github repository contains code and instructions for calculating personalized Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia. Details of the method are described in the article:
A neuroimaging biomarker for striatal dysfunction in schizophrenia. Nat Med (2020). https://doi.org/10.1038/s41591-020-0793-8
Getting Started
  • FSA is currently developed based on Python 2.X, requiring Python packages scipy, nilearn, sklearn, and joblib.
  • Please download the essential materials (e.g. SVM model) from figshare.
  • The FSA is currently developed and validated using the resting-state MRI data preprocessed by a open-source tool BRANT. Briefly, the raw fMRI image was preprocessed by slice timing, realign, coregister, normalization and denoising. Our model was validated based on the preprocessed fMRI images with global signal regression ('fdGSRwra*') and normalized fALFF images ('fALFF_z_').
  • Once established prerequisites above, personalized FSA score can be easily calculated parallelly following instructions and code in fsa.ipynb.
When using BRANT, please cite:
Copyright Information
The materials and code to calculate personalized FSA score is available for noncommercial use and exclusively for research purpose. For potential commercial use, please contact Bing Liu at bing.liu@bnu.edu.cn.
About
Calculation of Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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FSA
This is a Github repository contains code and instructions for calculating personalized Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia. Details of the method are described in the article:
A neuroimaging biomarker for striatal dysfunction in schizophrenia. Nat Med (2020). https://doi.org/10.1038/s41591-020-0793-8
Getting Started
  • FSA is currently developed based on Python 2.X, requiring Python packages scipy, nilearn, sklearn, and joblib.
  • Please download the essential materials (e.g. SVM model) from figshare.
  • The FSA is currently developed and validated using the resting-state MRI data preprocessed by a open-source tool BRANT. Briefly, the raw fMRI image was preprocessed by slice timing, realign, coregister, normalization and denoising. Our model was validated based on the preprocessed fMRI images with global signal regression ('fdGSRwra*') and normalized fALFF images ('fALFF_z_').
  • Once established prerequisites above, personalized FSA score can be easily calculated parallelly following instructions and code in fsa.ipynb.
When using BRANT, please cite:
Copyright Information
The materials and code to calculate personalized FSA score is available for noncommercial use and exclusively for research purpose. For potential commercial use, please contact Bing Liu at bing.liu@bnu.edu.cn.
About
Calculation of Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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FSA
This is a Github repository contains code and instructions for calculating personalized Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia. Details of the method are described in the article:
A neuroimaging biomarker for striatal dysfunction in schizophrenia. Nat Med (2020). https://doi.org/10.1038/s41591-020-0793-8
Getting Started
  • FSA is currently developed based on Python 2.X, requiring Python packages scipy, nilearn, sklearn, and joblib.
  • Please download the essential materials (e.g. SVM model) from figshare.
  • The FSA is currently developed and validated using the resting-state MRI data preprocessed by a open-source tool BRANT. Briefly, the raw fMRI image was preprocessed by slice timing, realign, coregister, normalization and denoising. Our model was validated based on the preprocessed fMRI images with global signal regression ('fdGSRwra*') and normalized fALFF images ('fALFF_z_').
  • Once established prerequisites above, personalized FSA score can be easily calculated parallelly following instructions and code in fsa.ipynb.
When using BRANT, please cite:
Copyright Information
The materials and code to calculate personalized FSA score is available for noncommercial use and exclusively for research purpose. For potential commercial use, please contact Bing Liu at bing.liu@bnu.edu.cn.
About
Calculation of Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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FSA
This is a Github repository contains code and instructions for calculating personalized Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia. Details of the method are described in the article:
A neuroimaging biomarker for striatal dysfunction in schizophrenia. Nat Med (2020). https://doi.org/10.1038/s41591-020-0793-8
Getting Started
  • FSA is currently developed based on Python 2.X, requiring Python packages scipy, nilearn, sklearn, and joblib.
  • Please download the essential materials (e.g. SVM model) from figshare.
  • The FSA is currently developed and validated using the resting-state MRI data preprocessed by a open-source tool BRANT. Briefly, the raw fMRI image was preprocessed by slice timing, realign, coregister, normalization and denoising. Our model was validated based on the preprocessed fMRI images with global signal regression ('fdGSRwra*') and normalized fALFF images ('fALFF_z_').
  • Once established prerequisites above, personalized FSA score can be easily calculated parallelly following instructions and code in fsa.ipynb.
When using BRANT, please cite:
Copyright Information
The materials and code to calculate personalized FSA score is available for noncommercial use and exclusively for research purpose. For potential commercial use, please contact Bing Liu at bing.liu@bnu.edu.cn.
About
Calculation of Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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FSA
This is a Github repository contains code and instructions for calculating personalized Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia. Details of the method are described in the article:
A neuroimaging biomarker for striatal dysfunction in schizophrenia. Nat Med (2020). https://doi.org/10.1038/s41591-020-0793-8
Getting Started
  • FSA is currently developed based on Python 2.X, requiring Python packages scipy, nilearn, sklearn, and joblib.
  • Please download the essential materials (e.g. SVM model) from figshare.
  • The FSA is currently developed and validated using the resting-state MRI data preprocessed by a open-source tool BRANT. Briefly, the raw fMRI image was preprocessed by slice timing, realign, coregister, normalization and denoising. Our model was validated based on the preprocessed fMRI images with global signal regression ('fdGSRwra*') and normalized fALFF images ('fALFF_z_').
  • Once established prerequisites above, personalized FSA score can be easily calculated parallelly following instructions and code in fsa.ipynb.
When using BRANT, please cite:
Copyright Information
The materials and code to calculate personalized FSA score is available for noncommercial use and exclusively for research purpose. For potential commercial use, please contact Bing Liu at bing.liu@bnu.edu.cn.
About
Calculation of Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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FSA
This is a Github repository contains code and instructions for calculating personalized Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia. Details of the method are described in the article:
A neuroimaging biomarker for striatal dysfunction in schizophrenia. Nat Med (2020). https://doi.org/10.1038/s41591-020-0793-8
Getting Started
  • FSA is currently developed based on Python 2.X, requiring Python packages scipy, nilearn, sklearn, and joblib.
  • Please download the essential materials (e.g. SVM model) from figshare.
  • The FSA is currently developed and validated using the resting-state MRI data preprocessed by a open-source tool BRANT. Briefly, the raw fMRI image was preprocessed by slice timing, realign, coregister, normalization and denoising. Our model was validated based on the preprocessed fMRI images with global signal regression ('fdGSRwra*') and normalized fALFF images ('fALFF_z_').
  • Once established prerequisites above, personalized FSA score can be easily calculated parallelly following instructions and code in fsa.ipynb.
When using BRANT, please cite:
Copyright Information
The materials and code to calculate personalized FSA score is available for noncommercial use and exclusively for research purpose. For potential commercial use, please contact Bing Liu at bing.liu@bnu.edu.cn.
About
Calculation of Functional Striatal Abnormalities (FSA) score for individuals with schizophrenia
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