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An example BIDS App (template repository)

Every BIDS App needs to follow a minimal set of command arguments common across all of the Apps. This allows users and developers to easily use and integrate BIDS Apps with their environment.

This is a minimalist example of a BIDS App consisting of a Dockerfile and a simple entry point script (written in this case in Python) accepting the standard BIDS Apps command line arguments. This repository can be used as a template for new BIDS Apps.

For more information about the specification of BIDS Apps see here.

Description

This is a placeholder for a short description explaining to the user what your App will doing.

Documentation

Provide a link to the documentation of your pipeline.

How to report errors

Provide instructions for users on how to get help and report errors.

Acknowledgments

Describe how would you would like users to acknowledge use of your App in their papers (citation, a paragraph that can be copy pasted, etc.)

Usage

This App has the following command line arguments:

	usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
bids_dir output_dir {participant,group}
Example BIDS App entry point script.
positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir The directory where the output files should be stored.
If you are running a group level analysis, this folder
should be prepopulated with the results of
the participant level analysis.
{participant,group} Level of the analysis that will be performed. Multiple
participant level analyses can be run independently
(in parallel).
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
analyzed. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects will be analyzed. Multiple participants
can be specified with a space separated list.

To run it in participant level mode (for one participant):

docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs participant --participant_label 01

After doing this for all subjects (potentially in parallel), the group level analysis can be run:

docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs group

Special considerations

Describe whether your app has any special requirements. For example:

  • Multiple map reduce steps (participant, group, participant2, group2 etc.)
  • Unusual memory requirements
  • etc.

About

This an example app that can serve as a template.

doi.org/10.1371/journal.pcbi.1005209

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Readme
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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" + '

Skip to content
BranchesTags
Repository files navigation
An example BIDS App (template repository)
Every BIDS App needs to follow a minimal set of command arguments common across
all of the Apps. This allows users and developers to easily use and integrate
BIDS Apps with their environment.
This is a minimalist example of a BIDS App consisting of a Dockerfile and a simple
entry point script (written in this case in Python) accepting the standard BIDS
Apps command line arguments. This repository can be used as a template for new BIDS Apps.
For more information about the specification of BIDS Apps see here.
Description
This is a placeholder for a short description explaining to the user what your App will doing.
Documentation
Provide a link to the documentation of your pipeline.
How to report errors
Provide instructions for users on how to get help and report errors.
Acknowledgments
Describe how would you would like users to acknowledge use of your App in their papers (citation, a paragraph that can be copy pasted, etc.)
Usage
This App has the following command line arguments:
	usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
bids_dir output_dir {participant,group}
Example BIDS App entry point script.
positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir The directory where the output files should be stored.
If you are running a group level analysis, this folder
should be prepopulated with the results of
the participant level analysis.
{participant,group} Level of the analysis that will be performed. Multiple
participant level analyses can be run independently
(in parallel).
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
analyzed. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects will be analyzed. Multiple participants
can be specified with a space separated list.

To run it in participant level mode (for one participant):
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs participant --participant_label 01

After doing this for all subjects (potentially in parallel), the group level analysis
can be run:
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs group

Special considerations
Describe whether your app has any special requirements. For example:
  • Multiple map reduce steps (participant, group, participant2, group2 etc.)
  • Unusual memory requirements
  • etc.
About
This an example app that can serve as a template.
doi.org/10.1371/journal.pcbi.1005209
Resources
Readme
Apache-2.0 license
Activity
Stars
0 stars
Watchers
0 watching
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0 forks
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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); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
An example BIDS App (template repository)
Every BIDS App needs to follow a minimal set of command arguments common across
all of the Apps. This allows users and developers to easily use and integrate
BIDS Apps with their environment.
This is a minimalist example of a BIDS App consisting of a Dockerfile and a simple
entry point script (written in this case in Python) accepting the standard BIDS
Apps command line arguments. This repository can be used as a template for new BIDS Apps.
For more information about the specification of BIDS Apps see here.
Description
This is a placeholder for a short description explaining to the user what your App will doing.
Documentation
Provide a link to the documentation of your pipeline.
How to report errors
Provide instructions for users on how to get help and report errors.
Acknowledgments
Describe how would you would like users to acknowledge use of your App in their papers (citation, a paragraph that can be copy pasted, etc.)
Usage
This App has the following command line arguments:
	usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
bids_dir output_dir {participant,group}
Example BIDS App entry point script.
positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir The directory where the output files should be stored.
If you are running a group level analysis, this folder
should be prepopulated with the results of
the participant level analysis.
{participant,group} Level of the analysis that will be performed. Multiple
participant level analyses can be run independently
(in parallel).
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
analyzed. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects will be analyzed. Multiple participants
can be specified with a space separated list.

To run it in participant level mode (for one participant):
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs participant --participant_label 01

After doing this for all subjects (potentially in parallel), the group level analysis
can be run:
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs group

Special considerations
Describe whether your app has any special requirements. For example:
  • Multiple map reduce steps (participant, group, participant2, group2 etc.)
  • Unusual memory requirements
  • etc.
About
This an example app that can serve as a template.
doi.org/10.1371/journal.pcbi.1005209
Resources
Readme
Apache-2.0 license
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
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Contributors
Languages

, '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); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
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An example BIDS App (template repository)
Every BIDS App needs to follow a minimal set of command arguments common across
all of the Apps. This allows users and developers to easily use and integrate
BIDS Apps with their environment.
This is a minimalist example of a BIDS App consisting of a Dockerfile and a simple
entry point script (written in this case in Python) accepting the standard BIDS
Apps command line arguments. This repository can be used as a template for new BIDS Apps.
For more information about the specification of BIDS Apps see here.
Description
This is a placeholder for a short description explaining to the user what your App will doing.
Documentation
Provide a link to the documentation of your pipeline.
How to report errors
Provide instructions for users on how to get help and report errors.
Acknowledgments
Describe how would you would like users to acknowledge use of your App in their papers (citation, a paragraph that can be copy pasted, etc.)
Usage
This App has the following command line arguments:
	usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
bids_dir output_dir {participant,group}
Example BIDS App entry point script.
positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir The directory where the output files should be stored.
If you are running a group level analysis, this folder
should be prepopulated with the results of
the participant level analysis.
{participant,group} Level of the analysis that will be performed. Multiple
participant level analyses can be run independently
(in parallel).
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
analyzed. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects will be analyzed. Multiple participants
can be specified with a space separated list.

To run it in participant level mode (for one participant):
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs participant --participant_label 01

After doing this for all subjects (potentially in parallel), the group level analysis
can be run:
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs group

Special considerations
Describe whether your app has any special requirements. For example:
  • Multiple map reduce steps (participant, group, participant2, group2 etc.)
  • Unusual memory requirements
  • etc.
About
This an example app that can serve as a template.
doi.org/10.1371/journal.pcbi.1005209
Resources
Readme
Apache-2.0 license
Activity
Stars
0 stars
Watchers
0 watching
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0 forks
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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" + '

Skip to content
BranchesTags
Repository files navigation
An example BIDS App (template repository)
Every BIDS App needs to follow a minimal set of command arguments common across
all of the Apps. This allows users and developers to easily use and integrate
BIDS Apps with their environment.
This is a minimalist example of a BIDS App consisting of a Dockerfile and a simple
entry point script (written in this case in Python) accepting the standard BIDS
Apps command line arguments. This repository can be used as a template for new BIDS Apps.
For more information about the specification of BIDS Apps see here.
Description
This is a placeholder for a short description explaining to the user what your App will doing.
Documentation
Provide a link to the documentation of your pipeline.
How to report errors
Provide instructions for users on how to get help and report errors.
Acknowledgments
Describe how would you would like users to acknowledge use of your App in their papers (citation, a paragraph that can be copy pasted, etc.)
Usage
This App has the following command line arguments:
	usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
bids_dir output_dir {participant,group}
Example BIDS App entry point script.
positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir The directory where the output files should be stored.
If you are running a group level analysis, this folder
should be prepopulated with the results of
the participant level analysis.
{participant,group} Level of the analysis that will be performed. Multiple
participant level analyses can be run independently
(in parallel).
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
analyzed. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects will be analyzed. Multiple participants
can be specified with a space separated list.

To run it in participant level mode (for one participant):
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs participant --participant_label 01

After doing this for all subjects (potentially in parallel), the group level analysis
can be run:
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs group

Special considerations
Describe whether your app has any special requirements. For example:
  • Multiple map reduce steps (participant, group, participant2, group2 etc.)
  • Unusual memory requirements
  • etc.
About
This an example app that can serve as a template.
doi.org/10.1371/journal.pcbi.1005209
Resources
Readme
Apache-2.0 license
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
An example BIDS App (template repository)
Every BIDS App needs to follow a minimal set of command arguments common across
all of the Apps. This allows users and developers to easily use and integrate
BIDS Apps with their environment.
This is a minimalist example of a BIDS App consisting of a Dockerfile and a simple
entry point script (written in this case in Python) accepting the standard BIDS
Apps command line arguments. This repository can be used as a template for new BIDS Apps.
For more information about the specification of BIDS Apps see here.
Description
This is a placeholder for a short description explaining to the user what your App will doing.
Documentation
Provide a link to the documentation of your pipeline.
How to report errors
Provide instructions for users on how to get help and report errors.
Acknowledgments
Describe how would you would like users to acknowledge use of your App in their papers (citation, a paragraph that can be copy pasted, etc.)
Usage
This App has the following command line arguments:
	usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
bids_dir output_dir {participant,group}
Example BIDS App entry point script.
positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir The directory where the output files should be stored.
If you are running a group level analysis, this folder
should be prepopulated with the results of
the participant level analysis.
{participant,group} Level of the analysis that will be performed. Multiple
participant level analyses can be run independently
(in parallel).
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
analyzed. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects will be analyzed. Multiple participants
can be specified with a space separated list.

To run it in participant level mode (for one participant):
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs participant --participant_label 01

After doing this for all subjects (potentially in parallel), the group level analysis
can be run:
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs group

Special considerations
Describe whether your app has any special requirements. For example:
  • Multiple map reduce steps (participant, group, participant2, group2 etc.)
  • Unusual memory requirements
  • etc.
About
This an example app that can serve as a template.
doi.org/10.1371/journal.pcbi.1005209
Resources
Readme
Apache-2.0 license
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
An example BIDS App (template repository)
Every BIDS App needs to follow a minimal set of command arguments common across
all of the Apps. This allows users and developers to easily use and integrate
BIDS Apps with their environment.
This is a minimalist example of a BIDS App consisting of a Dockerfile and a simple
entry point script (written in this case in Python) accepting the standard BIDS
Apps command line arguments. This repository can be used as a template for new BIDS Apps.
For more information about the specification of BIDS Apps see here.
Description
This is a placeholder for a short description explaining to the user what your App will doing.
Documentation
Provide a link to the documentation of your pipeline.
How to report errors
Provide instructions for users on how to get help and report errors.
Acknowledgments
Describe how would you would like users to acknowledge use of your App in their papers (citation, a paragraph that can be copy pasted, etc.)
Usage
This App has the following command line arguments:
	usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
bids_dir output_dir {participant,group}
Example BIDS App entry point script.
positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir The directory where the output files should be stored.
If you are running a group level analysis, this folder
should be prepopulated with the results of
the participant level analysis.
{participant,group} Level of the analysis that will be performed. Multiple
participant level analyses can be run independently
(in parallel).
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
analyzed. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects will be analyzed. Multiple participants
can be specified with a space separated list.

To run it in participant level mode (for one participant):
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs participant --participant_label 01

After doing this for all subjects (potentially in parallel), the group level analysis
can be run:
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs group

Special considerations
Describe whether your app has any special requirements. For example:
  • Multiple map reduce steps (participant, group, participant2, group2 etc.)
  • Unusual memory requirements
  • etc.
About
This an example app that can serve as a template.
doi.org/10.1371/journal.pcbi.1005209
Resources
Readme
Apache-2.0 license
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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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An example BIDS App (template repository)
Every BIDS App needs to follow a minimal set of command arguments common across
all of the Apps. This allows users and developers to easily use and integrate
BIDS Apps with their environment.
This is a minimalist example of a BIDS App consisting of a Dockerfile and a simple
entry point script (written in this case in Python) accepting the standard BIDS
Apps command line arguments. This repository can be used as a template for new BIDS Apps.
For more information about the specification of BIDS Apps see here.
Description
This is a placeholder for a short description explaining to the user what your App will doing.
Documentation
Provide a link to the documentation of your pipeline.
How to report errors
Provide instructions for users on how to get help and report errors.
Acknowledgments
Describe how would you would like users to acknowledge use of your App in their papers (citation, a paragraph that can be copy pasted, etc.)
Usage
This App has the following command line arguments:
	usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
bids_dir output_dir {participant,group}
Example BIDS App entry point script.
positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir The directory where the output files should be stored.
If you are running a group level analysis, this folder
should be prepopulated with the results of
the participant level analysis.
{participant,group} Level of the analysis that will be performed. Multiple
participant level analyses can be run independently
(in parallel).
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be
analyzed. The label corresponds to
sub-<participant_label> from the BIDS spec (so it does
not include "sub-"). If this parameter is not provided
all subjects will be analyzed. Multiple participants
can be specified with a space separated list.

To run it in participant level mode (for one participant):
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs participant --participant_label 01

After doing this for all subjects (potentially in parallel), the group level analysis
can be run:
docker run -i --rm \
-v /Users/filo/data/ds005:/bids_dataset:ro \
-v /Users/filo/outputs:/outputs \
bids/example \
/bids_dataset /outputs group

Special considerations
Describe whether your app has any special requirements. For example:
  • Multiple map reduce steps (participant, group, participant2, group2 etc.)
  • Unusual memory requirements
  • etc.
About
This an example app that can serve as a template.
doi.org/10.1371/journal.pcbi.1005209
Resources
Readme
Apache-2.0 license
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages