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Remi-GauRemi-Gau
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[FIX] properly identify run level contrasts (#1273)
* add build docker workflow * switch docker * fix contrast name regex for run level * update regex * update doc for naming of run and subject level contrasts * get results compare sessions * update doc * rm comments * fix test
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‎.github/workflows/docker.yml‎

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---
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name: docker
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on:
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push:
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branches: [main]
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tags: ['*']
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pull_request:
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branches: ['*']
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release:
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types: [published]
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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permissions:
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contents: read
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env:
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USER_NAME: cpplab
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REPO_NAME: bidspm
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# DATA: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
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IMAGE: /home/runner/work/bidspm/docker
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IS_TAGGED: ${{ github.ref_type == 'tag' }}
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IS_MAIN: ${{ github.ref == 'refs/heads/main' }}
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jobs:
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docker-build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Build the Docker image
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run: |
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docker build . --file Dockerfile --tag ${{env.USER_NAME}}/${{env.REPO_NAME}}
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mkdir -p ${{ env.IMAGE }}
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docker save "${{env.USER_NAME}}/${{env.REPO_NAME}}" > "${{ env.IMAGE }}/image.tar"
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docker images
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- name: Upload docker artifacts
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uses: actions/upload-artifact@v4
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with:
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name: docker
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path: ${{ env.IMAGE }}
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docker-run:
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runs-on: ubuntu-latest
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needs: [docker-build]
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steps:
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- name: Restore docker image
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uses: actions/download-artifact@v4
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with:
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name: docker
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path: ${{ env.IMAGE }}
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- name: Test the Docker image
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run: |
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docker load -i ${{ env.IMAGE }}/image.tar
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docker run --rm \
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${{env.USER_NAME}}/${{env.REPO_NAME}} \
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--help
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docker run --rm \
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${{env.USER_NAME}}/${{env.REPO_NAME}} \
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--version
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docker-push:
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runs-on: ubuntu-latest
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needs: [docker-run]
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steps:
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- name: Log in to Docker Hub
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uses: docker/[email protected]
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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- name: Restore docker image
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uses: actions/download-artifact@v4
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with:
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name: docker
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path: ${{ env.IMAGE }}
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- name: Load image
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run: docker load -i ${{ env.IMAGE }}/image.tar
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- name: Push unstable to dockerhub on tags or on main
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if: ${{ env.IS_MAIN == 'true' || env.IS_TAGGED == 'true' }}
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run: |
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echo "Pushing unstable versions to DockerHub"
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unstable="${{env.USER_NAME}}/${{env.REPO_NAME}}:unstable"
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docker tag "${{env.USER_NAME}}/${{env.REPO_NAME}}" "${unstable}"
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docker push "${unstable}"
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- name: Push stable release to dockerhub on tags only
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if: ${{ env.IS_TAGGED == 'true' }}
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run: |
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echo "Pushing stable and latest versions to DockerHub for latest and ${{ github.ref_name }}"
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unstable="${{env.USER_NAME}}/${{env.REPO_NAME}}:unstable"
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latest="${{env.USER_NAME}}/${{env.REPO_NAME}}:latest"
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docker tag "${unstable}" "${latest}"
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docker push "${latest}"
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tagged_release="${{env.USER_NAME}}/${{env.REPO_NAME}}:${{ github.ref_name }}"
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docker tag "${unstable}" "${tagged_release}"
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docker push "${tagged_release}"

‎.github/workflows/system_tests_bms.m‎

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cd(fullfile(root_dir, 'demos', 'bayes'));
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run ds000114_run;
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run ds000114_bayes_run;

‎bidspm.m‎

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function value = lowLevelActions()
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value = {'init'; ...
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'uninit'; ...
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'dev'
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'dev'; ...
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'version'; ...
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'run_tests'; ...
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'update'; ...
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'stats'; ...
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'contrasts'; ...
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'results'; ...
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'specify_only', ...
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'specify_only'; ...
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'bms'; ...
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'bms-posterior'; ...
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'bms-bms'};

‎demos/openneuro/Makefile‎

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mkdir -p inputs
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cd inputs && datalad install ///openneuro/ds000001
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cd inputs && datalad install ///openneuro-derivatives/ds000001-fmriprep
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cd inputs/ds000001 && datalad get sub-0[1-2] -J 3
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cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*tsv -J 12
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cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*json -J 12
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cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/anat/*MNI*desc-preproc*.nii.gz -J 12
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cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*MNI*desc-preproc*.nii.gz -J 12
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cd inputs/ds000001-fmriprep && datalad get sub-0[1-2]/func/*MNI*desc-*bold.nii.gz -J 12
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cd inputs/ds000001 && datalad get sub-0[1-5] -J 3
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cd inputs/ds000001-fmriprep && datalad get sub-0[1-5]/func/*tsv -J 12
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cd inputs/ds000001-fmriprep && datalad get sub-0[1-5]/func/*json -J 12
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cd inputs/ds000001-fmriprep && datalad get sub-0[1-5]/anat/*MNI*desc-preproc*.nii.gz -J 12
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cd inputs/ds000001-fmriprep && datalad get sub-0[1-5]/func/*MNI*desc-preproc*.nii.gz -J 12
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cd inputs/ds000001-fmriprep && datalad get sub-0[1-3]/func/*MNI*desc-*bold.nii.gz -J 12
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data_ds000114:
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mkdir -p inputs

‎demos/openneuro/ds000001_aroma_run.m‎

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fmriprep_dir = fullfile(root_dir, 'inputs', 'ds000001-fmriprep');
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output_dir = fullfile(root_dir, 'outputs', 'ds000001', 'derivatives');
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participant_label = {'01', '02', '03', '04', '05'};
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participant_label = {'01', '02', '03'};
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task = {'balloonanalogrisktask'};
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space = {'MNI152NLin6Asym'};
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‎demos/openneuro/ds000001_smooth_run.m‎

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% Runs:
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% - smoothing of fmriprep data
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% - stats at the suject level
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% - stats at the group level
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%
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% (C) Copyright 2020 bidspm developers
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fmriprep_dir = fullfile(root_dir, 'inputs', 'ds000001-fmriprep');
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output_dir = fullfile(root_dir, 'outputs', 'ds000001', 'derivatives');
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participant_label = {'01', '02', '03', '04', '05'};
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participant_label = {'01', '02', '03'};
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task = {'balloonanalogrisktask'};
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space = {'MNI152NLin2009cAsym'};
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‎demos/openneuro/models/model-balloonanalogrisktaskDefault_smdl.json‎

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"X": [
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1
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],
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"Type": "glm"
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"Type": "glm",
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"Software": {
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"bidspm": {
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"Results": [
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{
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"name": [
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"cash_demean"
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],
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"nidm": false
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}
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]
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}
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}
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},
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"DummyContrasts": {
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"Test": "t"

‎demos/openneuro/models/model-ds000114_desc-testRetestLineBisection_smdl.json‎

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"X": [
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1
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],
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"Type": "glm"
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"Type": "glm",
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"Software": {
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"bidspm": {
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"Results": [
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{
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"name": [
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"Correct_Task",
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"TaskResponded_gt_CtrlResponded"
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]
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}
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]
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}
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}
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},
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"DummyContrasts": {
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"Test": "t"
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"session",
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1
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],
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"Type": "glm"
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"Type": "glm",
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"Software": {
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"bidspm": {
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"Results": [
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{
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"name": [
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"test_gt_retest-TaskResponded_gt_CtrlResponded"
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]
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}
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]
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}
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}
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},
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"Contrasts": [
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{

‎docs/source/demos/openneuro.md‎

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- several tasks
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- several sessions
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- one or several runs depending on task
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- fmriprep data
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### Scripts
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- [Source dataset](https://openneuro.org/datasets/ds000224)
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### Features
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- fmriprep data
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### Scripts
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```{eval-rst}

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