diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml new file mode 100644 index 0000000..b1378e9 --- /dev/null +++ b/.github/workflows/deploy.yml @@ -0,0 +1,75 @@ +name: deploy + +on: + pull_request: + paths: + - ".github/workflows/deploy.yml" + - "404.html" + - "Gemfile" + - "_config.yml" + - "_layouts/**" + - "_posts/**" + - "about.md" + - "index.html" + push: + branches: + - main + paths: + - ".github/workflows/deploy.yml" + - "404.html" + - "Gemfile" + - "_config.yml" + - "_layouts/**" + - "_posts/**" + - "about.md" + - "index.html" + workflow_dispatch: + +permissions: + contents: read + pages: write + id-token: write + +concurrency: + group: pages + cancel-in-progress: true + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Set up Ruby + uses: ruby/setup-ruby@v1 + with: + ruby-version: "3.2" + bundler-cache: true + + - name: Configure Pages + uses: actions/configure-pages@v5 + + - name: Build site + env: + JEKYLL_ENV: production + run: bundle exec jekyll build + + - name: Upload Pages artifact + uses: actions/upload-pages-artifact@v3 + with: + path: ./_site + + deploy: + if: github.event_name != 'pull_request' + needs: build + runs-on: ubuntu-latest + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 diff --git a/.gitignore b/.gitignore index e77313b..4f27c85 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,6 @@ _site/ -Gemfile* +vendor/bundle/ +.bundle/ # Byte-compiled / optimized / DLL files __pycache__/ diff --git a/404.html b/404.html new file mode 100644 index 0000000..086a5c9 --- /dev/null +++ b/404.html @@ -0,0 +1,25 @@ +--- +permalink: /404.html +layout: default +--- + + + +
+

404

+ +

Page not found :(

+

The requested page could not be found.

+
diff --git a/Gemfile b/Gemfile new file mode 100644 index 0000000..9bfdf55 --- /dev/null +++ b/Gemfile @@ -0,0 +1,20 @@ +source "https://rubygems.org" +gem "github-pages", "~> 231", group: :jekyll_plugins + +group :jekyll_plugins do + gem "jekyll-feed", "~> 0.12" +end + +# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem +# and associated library. +platforms :mingw, :x64_mingw, :mswin, :jruby do + gem "tzinfo", ">= 1", "< 3" + gem "tzinfo-data" +end + +# Performance-booster for watching directories on Windows +gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin] + +# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem +# do not have a Java counterpart. +gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby] diff --git a/Gemfile.lock b/Gemfile.lock new file mode 100644 index 0000000..0a1e4d8 --- /dev/null +++ b/Gemfile.lock @@ -0,0 +1,425 @@ +GEM + remote: https://rubygems.org/ + specs: + activesupport 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If you find +# yourself editing this file very often, consider using Jekyll's data files +# feature for the data you need to update frequently. +# +# For technical reasons, this file is *NOT* reloaded automatically when you use +# 'bundle exec jekyll serve'. If you change this file, please restart the server process. +# +# If you need help with YAML syntax, here are some quick references for you: +# https://learn-the-web.algonquindesign.ca/topics/markdown-yaml-cheat-sheet/#yaml +# https://learnxinyminutes.com/docs/yaml/ +# +# Site settings +# These are used to personalize your new site. If you look in the HTML files, +# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on. +# You can create any custom variable you would like, and they will be accessible +# in the templates via {{ site.myvariable }}. + +title: Open Multi-Echo Datasets +description: >- + A summary of available open multi-echo fMRI datasets +baseurl: "/open-multi-echo-data" # the subpath of your site, e.g. /blog +url: "https://me-ica.github.io" # the base hostname & protocol for your site, e.g. http://example.com +repository_url: "https://github.com/ME-ICA/open-multi-echo-data" +repository_nwo: "ME-ICA/open-multi-echo-data" +owner_name: "ME-ICA" +owner_url: "https://github.com/ME-ICA" + +# Build settings +remote_theme: pages-themes/minimal@v0.2.0 +plugins: +- jekyll-remote-theme # add this line to the plugins list if you already have one + +# Exclude from processing. +# The following items will not be processed, by default. +# Any item listed under the `exclude:` key here will be automatically added to +# the internal "default list". +# +# Excluded items can be processed by explicitly listing the directories or +# their entries' file path in the `include:` list. +# +# exclude: +# - .sass-cache/ +# - .jekyll-cache/ +# - gemfiles/ +# - Gemfile +# - Gemfile.lock +# - node_modules/ +# - vendor/bundle/ +# - vendor/cache/ +# - vendor/gems/ +# - vendor/ruby/ diff --git a/_layouts/dataset.html b/_layouts/dataset.html new file mode 100644 index 0000000..7942d86 --- /dev/null +++ b/_layouts/dataset.html @@ -0,0 +1,54 @@ +--- +layout: default +--- + +

{{ page.title }}

+ + + + + + + + + + + + + + + + +
Magnetic Field StrengthNumber(s) of EchoesExtras
{{ page.scanner }}{{ page.echoes | join: ", " }} +
    + {% for extra in page.extras %} +
  • + {% if extra == "asl" %} + Concurrent ASL + {% elsif extra == "complex" %} + Complex-valued BOLD + {% elsif extra == "norf" %} + Noise scans + {% elsif extra == "physio" %} + Concurrent physiological monitoring + {% elsif extra == "single-echo" %} + Comparison single-echo BOLD + {% endif %} +
  • + {% endfor %} +
+
+ + +

Raw Dataset: {{ page.website }}

+{% if page.fmriprep %} +

fMRIPrep derivatives: {{ page.fmriprep }}

+{% endif %} +{% if page.afni %} +

AFNI derivatives: {{ page.afni }}

+{% endif %} +
+ +
+ +{{content}} diff --git a/_layouts/default.html b/_layouts/default.html new file mode 100644 index 0000000..f3ab310 --- /dev/null +++ b/_layouts/default.html @@ -0,0 +1,40 @@ + + + + + + + {{ page.title | default: site.title }} + + + + +
+
+

{{ site.title }}

+ {% if site.logo %} + Logo + {% endif %} +

{{ site.description }}

+ {% if site.repository_url %} +

View the Project on GitHub {{ site.repository_nwo }}

+ {% endif %} + {% if site.owner_url %} +

View the ME-ICA GitHub organization

+ {% endif %} +
+
+ {{ content }} +
+ +
+ + + diff --git a/_posts/2024-07-31-laion-fmri.md b/_posts/2024-07-31-laion-fmri.md new file mode 100644 index 0000000..afde160 --- /dev/null +++ b/_posts/2024-07-31-laion-fmri.md @@ -0,0 +1,21 @@ +--- +layout: dataset +title: "LAION-fMRI" +categories: dataset +website: https://laion-fmri.hebartlab.com/index.html +scanner: 7T +echoes: [3] +extras: [] +fmriprep: +afni: +--- + +Five participants. 25,052 launch-release images. 165 acquired 7T BOLD sessions with single-trial GLMsingle betas, retinotopy, localizers, and diffusion. + +https://laion-fmri.hebartlab.com/mri_acquisition.html + +5 participants. 30 scans each. +7T MRI +TR = 1900 ms +TE1 = 11.0 ms, TE2 = 28.82 ms, TE3 = 46.62 ms +1.8 mm isotropic diff --git a/_posts/2024-07-31-mhq3f.md b/_posts/2024-07-31-mhq3f.md new file mode 100644 index 0000000..ef182a3 --- /dev/null +++ b/_posts/2024-07-31-mhq3f.md @@ -0,0 +1,13 @@ +--- +layout: dataset +title: "MICA-PNI: Precision NeuroImaging and Connectomics" +categories: dataset +website: https://osf.io/mhq3f/ +scanner: 7T +echoes: [3] +extras: [] +fmriprep: +afni: +--- + +10 participants, 3 echoes, 3 sessions per participant, several different tasks diff --git a/_posts/2024-08-01-ds000210.md b/_posts/2024-08-01-ds000210.md new file mode 100644 index 0000000..42fe7c9 --- /dev/null +++ b/_posts/2024-08-01-ds000210.md @@ -0,0 +1,11 @@ +--- +layout: dataset +title: "Multi-echo fMRI replication sample of autobiographical memory, prospection and theory of mind reasoning tasks" +categories: dataset +website: https://openneuro.org/datasets/ds000210 +scanner: 3T +echoes: [3] +extras: [physio] +fmriprep: +afni: +--- diff --git a/_posts/2024-08-01-ds000216.md b/_posts/2024-08-01-ds000216.md new file mode 100644 index 0000000..f127335 --- /dev/null +++ b/_posts/2024-08-01-ds000216.md @@ -0,0 +1,11 @@ +--- +layout: dataset +title: "Multiband Multi-Echo Imaging of Simultaneous Oxygenation and Flow Timeseries for Resting State Connectivity" +categories: dataset +website: https://openneuro.org/datasets/ds000216 +scanner: 3T +echoes: [4] +extras: [asl] +fmriprep: +afni: +--- diff --git a/_posts/2024-08-01-ds000254.md b/_posts/2024-08-01-ds000254.md new file mode 100644 index 0000000..2d134e4 --- /dev/null +++ b/_posts/2024-08-01-ds000254.md @@ -0,0 +1,11 @@ +--- +layout: dataset +title: "Multiband Multi-Echo Simultaneous ASL/BOLD for task-induced functional MRI" +categories: dataset +website: https://openneuro.org/datasets/ds000254 +scanner: 3T +echoes: [4] +extras: [asl] +fmriprep: +afni: +--- diff --git a/_posts/2024-08-01-ds000258.md b/_posts/2024-08-01-ds000258.md new file mode 100644 index 0000000..92b449e --- /dev/null +++ b/_posts/2024-08-01-ds000258.md @@ -0,0 +1,11 @@ +--- +layout: dataset +title: "Multi-echo Cambridge" +categories: dataset +website: https://openneuro.org/datasets/ds000258 +scanner: 3T +echoes: [4] +extras: [] +fmriprep: +afni: +--- diff --git a/_posts/2024-08-01-ds001491.md b/_posts/2024-08-01-ds001491.md new file mode 100644 index 0000000..cfb11b3 --- /dev/null +++ b/_posts/2024-08-01-ds001491.md @@ -0,0 +1,11 @@ +--- +layout: dataset +title: "Valence processing differs across stimulus modalities" +categories: dataset +website: https://openneuro.org/datasets/ds001491 +scanner: 3T +echoes: [3] +extras: [] +fmriprep: +afni: +--- diff --git a/_posts/2024-08-01-ds002156.md b/_posts/2024-08-01-ds002156.md new file mode 100644 index 0000000..c34c00f --- /dev/null +++ b/_posts/2024-08-01-ds002156.md @@ -0,0 +1,11 @@ +--- +layout: dataset +title: "Multi-echo masking test dataset" +categories: dataset +website: https://openneuro.org/datasets/ds002156 +scanner: 3T +echoes: [4] +extras: [physio] +fmriprep: +afni: +--- diff --git a/_posts/2024-08-01-ds002278.md b/_posts/2024-08-01-ds002278.md new file mode 100644 index 0000000..f7d0777 --- /dev/null +++ b/_posts/2024-08-01-ds002278.md @@ -0,0 +1,11 @@ +--- +layout: dataset +title: "Dense Investigation of Variability of Affect (DIVA)" +categories: dataset +website: https://openneuro.org/datasets/ds002278 +scanner: 3T +echoes: [4] +extras: [complex, physio] +fmriprep: +afni: +--- diff --git a/_posts/2024-08-01-ds003192.md b/_posts/2024-08-01-ds003192.md new file mode 100644 index 0000000..385a9d0 --- /dev/null +++ b/_posts/2024-08-01-ds003192.md @@ -0,0 +1,11 @@ +--- +layout: dataset +title: "EuskalIBUR" +categories: dataset +website: https://openneuro.org/datasets/ds003192 +scanner: 3T +echoes: [5] +extras: [physio] +fmriprep: +afni: +--- diff --git a/_posts/2024-08-01-ds003592.md b/_posts/2024-08-01-ds003592.md new file mode 100644 index 0000000..763c939 --- /dev/null +++ b/_posts/2024-08-01-ds003592.md @@ -0,0 +1,14 @@ +--- +layout: dataset +title: "Neurocognitive aging data release with behavioral, structural, and multi-echo functional MRI measures" +categories: dataset +website: https://openneuro.org/datasets/ds003592 +scanner: 3T +echoes: [3] +extras: [physio] +fmriprep: +afni: +--- + +3 echoes, physio, 301 subjects + diff --git a/_posts/2024-08-01-ds003643.md b/_posts/2024-08-01-ds003643.md new file mode 100644 index 0000000..ab8dc1a --- /dev/null +++ b/_posts/2024-08-01-ds003643.md @@ -0,0 +1,11 @@ +--- +layout: dataset +title: "Le Petit Prince" +categories: dataset +website: https://openneuro.org/datasets/ds003643 +scanner: 3T +echoes: [3] +extras: [] +fmriprep: +afni: +--- diff --git a/_posts/2024-08-01-ds003823.md b/_posts/2024-08-01-ds003823.md new file mode 100644 index 0000000..fdf1592 --- /dev/null +++ b/_posts/2024-08-01-ds003823.md @@ -0,0 +1,13 @@ +--- +layout: dataset +title: "Heart rate variability biofeedback training and emotion regulation" +categories: dataset +website: https://openneuro.org/datasets/ds003823 +scanner: 3T +echoes: [3] +extras: [physio] +fmriprep: +afni: +--- + +3 echoes, physio, many different tasks, 177 participants diff --git a/_posts/2024-08-01-ds004499.md b/_posts/2024-08-01-ds004499.md new file mode 100644 index 0000000..9c74ff3 --- /dev/null +++ b/_posts/2024-08-01-ds004499.md @@ -0,0 +1,15 @@ +--- +layout: dataset +title: "Multi-echo simultaneous multislice fMRI dataset: Effect of acquisition parameters on fMRI data" +categories: dataset +website: https://openneuro.org/datasets/ds004499 +scanner: 3T +echoes: [3] +extras: [physio] +fmriprep: +afni: +--- + +Three echoes with concurrent physio, but they varied TR, MB factor, number of scans, and flip angle. + +The task is a combined flashing checkerboard-button pressing block design. diff --git a/_posts/2024-08-01-ds004627.md b/_posts/2024-08-01-ds004627.md new file mode 100644 index 0000000..2749672 --- /dev/null +++ b/_posts/2024-08-01-ds004627.md @@ -0,0 +1,11 @@ +--- +layout: dataset +title: "Characterization and Treatment of Adolescent Depression (CAT-D)" +categories: dataset +website: https://openneuro.org/datasets/ds004627 +scanner: 3T +echoes: [4] +extras: [physio] +fmriprep: +afni: +--- diff --git a/_posts/2024-08-01-ds004662.md b/_posts/2024-08-01-ds004662.md new file mode 100644 index 0000000..5eea898 --- /dev/null +++ b/_posts/2024-08-01-ds004662.md @@ -0,0 +1,13 @@ +--- +layout: dataset +title: "Denoising task-correlated head motion from motor-task fMRI data with multi-echo ICA" +categories: dataset +website: https://openneuro.org/datasets/ds004662 +scanner: 3T +echoes: [5] +extras: [physio] +fmriprep: https://openneuro.org/datasets/ds007661 +afni: +--- + +This dataset also has CO2, right-hand grip, and left-hand grip data. diff --git a/_posts/2024-08-01-ds004787.md b/_posts/2024-08-01-ds004787.md new file mode 100644 index 0000000..a6ce401 --- /dev/null +++ b/_posts/2024-08-01-ds004787.md @@ -0,0 +1,13 @@ +--- +layout: dataset +title: "NIMH METeR" +categories: dataset +website: https://openneuro.org/datasets/ds004787 +scanner: 3T +echoes: [4] +extras: [physio, single-echo] +fmriprep: +afni: +--- + +T1w, single-echo, and 4-echo multi-echo. diff --git a/_posts/2024-08-01-ds004935.md b/_posts/2024-08-01-ds004935.md new file mode 100644 index 0000000..0cf2f6f --- /dev/null +++ b/_posts/2024-08-01-ds004935.md @@ -0,0 +1,13 @@ +--- +layout: dataset +title: "Multivariate Assessment of Inhibitory Control in Youth: Links with Psychopathology and Brain Function Dataset" +categories: dataset +website: https://openneuro.org/datasets/ds004935 +scanner: 3T +echoes: [3] +extras: [] +fmriprep: +afni: +--- + +One run of resting-state with three echoes. diff --git a/_posts/2024-08-01-ds005085.md b/_posts/2024-08-01-ds005085.md new file mode 100644 index 0000000..74fdee2 --- /dev/null +++ b/_posts/2024-08-01-ds005085.md @@ -0,0 +1,13 @@ +--- +layout: dataset +title: "Sequence pilot: multiecho and multiband fMRI" +categories: dataset +website: https://openneuro.org/datasets/ds005085 +scanner: 3T +echoes: [4] +extras: [complex, single-echo] +fmriprep: +afni: +--- + +A comparison dataset of single-echo and four-echo multi-echo runs. Each run is either singleband, MB3, or MB6. The multi-echo runs have phase reconstruction. diff --git a/_posts/2024-08-01-ds005118.md b/_posts/2024-08-01-ds005118.md new file mode 100644 index 0000000..03e6ea2 --- /dev/null +++ b/_posts/2024-08-01-ds005118.md @@ -0,0 +1,15 @@ +--- +layout: dataset +title: "Weill Cornell Medicine Multi-echo (WCM-ME) Dataset" +categories: dataset +website: https://openneuro.org/datasets/ds005118 +scanner: 3T +echoes: [5] +extras: [] +fmriprep: +afni: +--- + +Five echoes, with 10 sessions- each containing 4 runs of resting-state. + +There are also six T1ws and six T2ws. diff --git a/_posts/2024-08-01-ds005123.md b/_posts/2024-08-01-ds005123.md new file mode 100644 index 0000000..f1633ee --- /dev/null +++ b/_posts/2024-08-01-ds005123.md @@ -0,0 +1,13 @@ +--- +layout: dataset +title: "Social Reward and Aging: A Preliminary Multi-echo fMRI and Diffusion Dataset" +categories: dataset +website: https://openneuro.org/datasets/ds005123 +scanner: 3T +echoes: [4] +extras: [complex] +fmriprep: +afni: +--- + +Four echoes, complex-valued BOLD. Five tasks. 114 participants. diff --git a/_posts/2024-08-01-ds005264.md b/_posts/2024-08-01-ds005264.md new file mode 100644 index 0000000..440c3cd --- /dev/null +++ b/_posts/2024-08-01-ds005264.md @@ -0,0 +1,13 @@ +--- +layout: dataset +title: "SoCal Kinesia and Incentivization for Parkinson's Disease (SKIP): Ultra-High Field Functional Connectivity" +categories: dataset +website: https://openneuro.org/datasets/ds005264 +scanner: 7T +echoes: [3] +extras: [physio] +fmriprep: +afni: +--- + +21 participants, 3 echoes, lots of physio, resting-state diff --git a/_posts/2024-08-01-ds005449.md b/_posts/2024-08-01-ds005449.md new file mode 100644 index 0000000..f6caef4 --- /dev/null +++ b/_posts/2024-08-01-ds005449.md @@ -0,0 +1,17 @@ +--- +layout: dataset +title: "Valenced tactile information is evoked by neutral visual cues following emotional learning" +categories: dataset +website: https://openneuro.org/datasets/ds005449 +scanner: 3T +echoes: [3] +extras: [] +fmriprep: +afni: +--- + +122 participants, 3 echoes. +There are a wide range of tasks. + +The tasks and runs are not named readably. +For example, in sub-001, there is only one rest run, but it's named run-05. diff --git a/_posts/2024-08-01-ds006072.md b/_posts/2024-08-01-ds006072.md new file mode 100644 index 0000000..c57b3c7 --- /dev/null +++ b/_posts/2024-08-01-ds006072.md @@ -0,0 +1,19 @@ +--- +layout: dataset +title: "Psilocybin Precision Functional Mapping" +categories: dataset +website: https://openneuro.org/datasets/ds006072 +scanner: 3T +echoes: [5] +extras: [complex, norf] +fmriprep: +afni: +--- + +11 participants, many sessions, 5 echoes, and magnitude+phase reconstruction. + +The noRF scans aren't split out of the BOLD files. + +They only shared NORDIC-denoised data. + +Many of the runs don't have phase data. diff --git a/_posts/2024-08-01-ds006131.md b/_posts/2024-08-01-ds006131.md new file mode 100644 index 0000000..f26ca54 --- /dev/null +++ b/_posts/2024-08-01-ds006131.md @@ -0,0 +1,17 @@ +--- +layout: dataset +title: "PAFIN: PennLINC AFfective INstability" +categories: dataset +website: https://openneuro.org/datasets/ds006131 +scanner: 3T +echoes: [5] +extras: [complex, norf, physio] +fmriprep: https://openneuro.org/datasets/ds006185 +afni: +--- + +10 participants, 5 echoes, magnitude+phase reconstruction, noRF files, and concurrent physiological recordings. + +This dataset will ultimately have 100 participants, but they will be released in batches. + +The first batch has 10 regular participants and 2 pilot subjects. diff --git a/_posts/2024-08-01-ds006693.md b/_posts/2024-08-01-ds006693.md new file mode 100644 index 0000000..97e803a --- /dev/null +++ b/_posts/2024-08-01-ds006693.md @@ -0,0 +1,18 @@ +--- +layout: dataset +title: "NODEAP: Distinct contributions of anterior and posterior OFC to outcome-guided behavior" +categories: dataset +website: https://openneuro.org/datasets/ds006693 +scanner: 3T +echoes: [3] +extras: [] +fmriprep: +afni: +--- + +48 participants, 3 echoes. + +A study testing differential roles of the anterior (aOFC) and posterior (pOFC) lateral orbitofrontal cortex in +outcome-guided (goal-directed) behavior. +Participants completed odor-reward learning and outcome devaluation across multiple sessions. +Network-targeted TMS was applied to aOFC or pOFC in separate sessions to probe effects on learning vs. value inference. diff --git a/_posts/2024-08-01-ds006707.md b/_posts/2024-08-01-ds006707.md new file mode 100644 index 0000000..401c07b --- /dev/null +++ b/_posts/2024-08-01-ds006707.md @@ -0,0 +1,14 @@ +--- +layout: dataset +title: "Night Owls Scan Club" +categories: dataset +website: https://openneuro.org/datasets/ds006707 +scanner: 3T +echoes: [4] +extras: [complex] +fmriprep: +afni: +--- + +Four participants, 12 sessions each. +The multi-echo data have magnitude+phase reconstruction and four echoes. diff --git a/_posts/2024-08-01-ds006926.md b/_posts/2024-08-01-ds006926.md new file mode 100644 index 0000000..caca25a --- /dev/null +++ b/_posts/2024-08-01-ds006926.md @@ -0,0 +1,20 @@ +--- +layout: dataset +title: "Complex multi-echo fMRI dataset: New strategies in processing of multi-echo data" +categories: dataset +website: https://openneuro.org/datasets/ds006926 +scanner: 3T +echoes: [3] +extras: [complex, physio] +fmriprep: +afni: +--- + +83 participants. +The multi-echo data have magnitude+phase reconstruction and three echoes. +The dataset also includes 10-echo MEGRE data. + +There are three tasks: resting-state, a visual oddball, and a visuo-motor task. +The physiological data includes electrocardiography and respiration. + +The data were acquired on two 3T Siemens Prisma scanners and scans were acquired with either TR=1800 ms or TR=800 ms. diff --git a/_posts/2024-08-01-ds006971.md b/_posts/2024-08-01-ds006971.md new file mode 100644 index 0000000..64203ea --- /dev/null +++ b/_posts/2024-08-01-ds006971.md @@ -0,0 +1,13 @@ +--- +layout: dataset +title: "Shoulder abduction motor-task fMRI in healthy participants" +categories: dataset +website: https://openneuro.org/datasets/ds006971 +scanner: 3T +echoes: [3] +extras: [] +fmriprep: +afni: +--- + +6 participants, with a shoulder abduction task. diff --git a/_posts/2024-08-01-ds007048.md b/_posts/2024-08-01-ds007048.md new file mode 100644 index 0000000..88766da --- /dev/null +++ b/_posts/2024-08-01-ds007048.md @@ -0,0 +1,20 @@ +--- +layout: dataset +title: "Whole-Brain Auditory Mapping with 3T Multi-Echo fMRI in healthy participants" +categories: dataset +website: https://openneuro.org/datasets/ds007048 +scanner: 3T +echoes: [3] +extras: [] +fmriprep: +afni: +--- + +14 participants. +12 participants have 1 session with 1 run of the auditory task. +3 participants have 2 sessions- the first has 1 run of auditory task and the second has 4 runs of the task. + +There are CO2 regressors in the derivatives, but they're not in the raw BIDS data. +I didn't label this dataset as having "physio" because I don't know if the CO2 regressors can be treated as raw data. + +Based on the preprint ([Medina et al., preprint](https://doi.org/10.64898/2026.06.29.735344)), I think that the ses-2 data from subjects 01, 02, and 03 is the same as the data for subjects 01, 02, and 03 in ds008070. diff --git a/_posts/2024-08-01-ds007407.md b/_posts/2024-08-01-ds007407.md new file mode 100644 index 0000000..ba88373 --- /dev/null +++ b/_posts/2024-08-01-ds007407.md @@ -0,0 +1,18 @@ +--- +layout: dataset +title: "Darkend Auditory Narrative Repeated Listening fMRI" +categories: dataset +website: https://openneuro.org/datasets/ds007407 +scanner: 3T +echoes: [3] +extras: [] +fmriprep: +afni: +--- + +36 participants. + +Participants listened to an auditory narrative ("Darkend of the Mall" from The Truth podcast) twice (darkend1 and darkend2). +Only the narrative listening portion of the scan is included in the events files. Post-narrative is not modeled. + +Data were acquired with TR = 1.0 s. The length of the stimulus is 18:25 min:sec (1105 TRs or seconds). Each task contains three echoes. diff --git a/_posts/2024-08-01-ds007486.md b/_posts/2024-08-01-ds007486.md new file mode 100644 index 0000000..37851d2 --- /dev/null +++ b/_posts/2024-08-01-ds007486.md @@ -0,0 +1,13 @@ +--- +layout: dataset +title: "Social Reward Processing, Response Inhibition, and Cue Reactivity in Problem Gamblers" +categories: dataset +website: https://openneuro.org/datasets/ds007486 +scanner: 3T +echoes: [4] +extras: [complex] +fmriprep: +afni: +--- + +Three tasks (SST, trust task, and passive ad viewing). Target of 60 participants (currently at 5). diff --git a/_posts/2024-08-01-ds007637.md b/_posts/2024-08-01-ds007637.md new file mode 100644 index 0000000..5f5f3a7 --- /dev/null +++ b/_posts/2024-08-01-ds007637.md @@ -0,0 +1,15 @@ +--- +layout: dataset +title: "Single-echo/multi-echo comparison pilot" +categories: dataset +website: https://openneuro.org/datasets/ds007637 +scanner: 3T +echoes: [5] +extras: [complex, norf, single-echo] +fmriprep: https://openneuro.org/datasets/ds007637 +afni: +--- + +8 participants with ~2 sessions, T1w, 2 runs of MBME resting-state, 2 runs of MBSE resting-state, 1 run of MBME Penn fractal n-back task. + +Multi-echo data have 5 echoes, magnitude+phase reconstruction, and 3 no-excitation volumes at the end, split out into noRF files. diff --git a/_posts/2024-08-01-ds008070.md b/_posts/2024-08-01-ds008070.md new file mode 100644 index 0000000..503c08f --- /dev/null +++ b/_posts/2024-08-01-ds008070.md @@ -0,0 +1,20 @@ +--- +layout: dataset +title: "Evaluating Approaches for Inference Testing of Whole-Brain Densely Sampled Single-Subject Task fMRI Data" +categories: dataset +website: https://openneuro.org/datasets/ds008070 +scanner: 3T +echoes: [3] +extras: [] +fmriprep: +afni: +--- + +5 participants with T1w, 4 runs of MBME auditory task. + +Multi-echo data have 3 echoes. + +There are CO2 regressors in the derivatives, but they're not in the raw BIDS data. +I didn't label this dataset as having "physio" because I don't know if the CO2 regressors can be treated as raw data. + +Based on the preprint ([Medina et al., preprint](https://doi.org/10.64898/2026.06.29.735344)), I think that the data from subjects 01, 02, and 03 is the same as the ses-2 data for subjects 01, 02, and 03 in ds007048. diff --git a/_posts/2024-08-01-ds008159.md b/_posts/2024-08-01-ds008159.md new file mode 100644 index 0000000..673ab46 --- /dev/null +++ b/_posts/2024-08-01-ds008159.md @@ -0,0 +1,18 @@ +--- +layout: dataset +title: "Stretch-Evoked Motor Responses in the Brainstem are Modulated by Task Instructions" +categories: dataset +website: https://openneuro.org/datasets/ds008159 +scanner: 3T +echoes: [3] +extras: [] +fmriprep: +afni: +--- + +26 participants with T1w, 2 runs of MBME yieldrest task. + +Multi-echo data have 3 echoes. + +There are CO2 regressors in the derivatives, but they're not in the raw BIDS data. +I didn't label this dataset as having "physio" because I don't know if the CO2 regressors can be treated as raw data. diff --git a/_posts/template.md b/_posts/template.md new file mode 100644 index 0000000..bd1c48f --- /dev/null +++ b/_posts/template.md @@ -0,0 +1,11 @@ +--- +layout: dataset +title: "" +categories: dataset +website: +scanner: +echoes: [] +extras: [] +fmriprep: +afni: +--- diff --git a/about.md b/about.md new file mode 100644 index 0000000..761ea0c --- /dev/null +++ b/about.md @@ -0,0 +1,9 @@ +--- +layout: default +title: About +permalink: /about/ +--- + +This site catalogs open multi-echo fMRI datasets and links to raw datasets and, when available, derivative outputs. + +Datasets are included here when they are freely available without registration or a data use agreement and contain more than two echoes in the BOLD time series. diff --git a/index.html b/index.html new file mode 100644 index 0000000..6bb9f8e --- /dev/null +++ b/index.html @@ -0,0 +1,357 @@ +--- +layout: default +title: Open Multi-Echo Datasets +--- +

{{ site.title }}

+ +This collects and describes every open multi-echo fMRI dataset that we know of. + +We define "open" as being freely available to the public without registration or a data use agreement. +This excludes several datasets that are fundamentally open, +but which have barriers to access that would prevent researchers from directly downloading the data. + +We define "multi-echo" as having more than two echoes in the BOLD time series. +This excludes two-echo datasets, which, though technically "multi-echo", cannot be analyzed with multi-echo methods. + +

Datasets ({{ site.categories.dataset.size }})

+ +{% assign echoes = "" | split: "" %} +{% assign extras = "" | split: "" %} +{% for post in site.categories.dataset %} + {% assign echoes = echoes | concat: post.echoes %} + {% assign extras = extras | concat: post.extras %} +{% endfor %} +{% assign echoes = echoes | uniq | sort %} +{% assign extras = extras | uniq | sort %} + + + + + + + + + + + + + + + + + + + + + {% for echo in echoes %} + + {% endfor %} + {% for extra in extras %} + + {% endfor %} + + + + + + {% for post in site.categories.dataset %} + + + + + + {% for echo in echoes %} + + {% endfor %} + {% for extra in extras %} + + {% endfor %} + + + + {% endfor %} + +
TitleURLScannerNumber of EchoesExtra FeaturesDerivatives
7T3T{{ echo }}{{ extra }}fMRIPrepAFNI
{{ post.title }}Dataset + {% if post.scanner == "7T" %} + X + {% endif %} + + {% if post.scanner == "3T" %} + X + {% endif %} + + {% if post.echoes contains echo %} + X + {% endif %} + + {% if post.extras contains extra %} + X + {% endif %} + + {% if post.fmriprep %} + X + {% endif %} + + {% if post.afni %} + X + {% endif %} +
+ +