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Merge branch 'dev' into cer-skullstrip_output
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‎.all-contributorsrc

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"infra",
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"design",
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"review",
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"bug"
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"bug",
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"test"
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]
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},
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{
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"contributions": [
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"bug",
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"content",
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"doc"
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"doc",
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"code",
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"review"
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]
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}
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],

‎.github/workflows/run_system_tests.yml

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name: system tests
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# Uses the cron schedule for github actions
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#
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# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
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#
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# ┌───────────── minute (0 - 59)
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# │ ┌───────────── hour (0 - 23)
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# │ │ ┌───────────── day of the month (1 - 31)
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# │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
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# │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
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# │ │ │ │ │
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# │ │ │ │ │
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# │ │ │ │ │
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# * * * * *
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on:
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push:
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branches:
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- master
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- main
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pull_request:
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branches:
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- 'master'
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- 'main'
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schedule:
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- cron: "* * 1 * *"
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env:
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OCTFLAGS: --no-gui --no-window-system --silent
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jobs:
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build:
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runs-on: ubuntu-20.04
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steps:
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- name: Install dependencies
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run: |
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sudo apt-get -y -qq update
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sudo apt-get -y install octave liboctave-dev
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sudo apt-get -y install nodejs npm
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- name: Clone cpp_spm
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uses: actions/checkout@v2
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with:
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submodules: true
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fetch-depth: 2
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- name: Install SPM
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run: |
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git clone https://github.com/spm/spm12.git --depth 1
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make -C spm12/src PLATFORM=octave distclean
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make -C spm12/src PLATFORM=octave
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make -C spm12/src PLATFORM=octave install
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octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
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- name: Update octave path
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run: |
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octave $OCTFLAGS --eval "initCppSpm; savepath();"
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- name: Prepare data
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run: |
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inputs_folder='demos/MoAE/inputs/'
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mkdir $inputs_folder
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curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $inputs_folder'MoAEpilot.zip'
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unzip $inputs_folder'MoAEpilot.zip' -d $inputs_folder
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mv $inputs_folder/MoAEpilot $inputs_folder/raw
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- name: Run system tests
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run: |
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cd demos/MoAE
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octave $OCTFLAGS --eval "MoAEpilot_run"
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‎.github/workflows/run_tests.yml

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name: tests and coverage
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# Uses the cron schedule for github actions
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#
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# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
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#
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# ┌───────────── minute (0 - 59)
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# │ ┌───────────── hour (0 - 23)
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# │ │ ┌───────────── day of the month (1 - 31)
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# │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
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# │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
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# │ │ │ │ │
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# │ │ │ │ │
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# │ │ │ │ │
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# * * * * *
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on:
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push:
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branches:
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- dev
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pull_request:
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branches: '*'
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schedule:
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- cron: "* * 1 * *"
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env:
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OCTFLAGS: --no-gui --no-window-system --silent
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jobs:
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build:
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runs-on: ubuntu-20.04
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steps:
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- name: Install dependencies
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run: |
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sudo apt-get -y -qq update
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sudo apt-get -y install octave liboctave-dev
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sudo apt-get -y install nodejs npm
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- name: Clone cpp_spm
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uses: actions/checkout@v2
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with:
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submodules: true
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fetch-depth: 2
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- name: Install SPM
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run: |
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git clone https://github.com/spm/spm12.git --depth 1
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make -C spm12/src PLATFORM=octave distclean
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make -C spm12/src PLATFORM=octave
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make -C spm12/src PLATFORM=octave install
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octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
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- name: Install Moxunit and MOcov
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run: |
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git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
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make -C MOxUnit install
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git clone https://github.com/MOcov/MOcov.git --depth 1
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make -C MOcov install
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- name: Update octave path
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run: |
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octave $OCTFLAGS --eval "initCppSpm; savepath();"
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octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();"
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- name: Prepare data
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run: |
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inputs_folder='demos/MoAE/inputs/'
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mkdir $inputs_folder
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curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $inputs_folder'MoAEpilot.zip'
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unzip $inputs_folder'MoAEpilot.zip' -d $inputs_folder
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mv $inputs_folder/MoAEpilot $inputs_folder/raw
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cd tests
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sh createDummyDataSet.sh
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cd ..
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- name: Run tests
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run: |
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octave $OCTFLAGS --eval "runTests"
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cat test_report.log | grep 0
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bash <(curl -s https://codecov.io/bash)
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‎.gitignore

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onsets*_events.mat
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# files in the demo folder related to running the demo analysis
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demos/*/*.zip
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demos/*/derivatives/*
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demos/MoAE/output/*
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demos/spm*/raw
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demos/spm*/source
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demos/*/outputs/
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demos/*/inputs/
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demos/*/*.nii
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demos/*/cfg/*.json
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# test folder and dummy data
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tests/sub-01/*
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tests/*.png
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tests/group/*
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tests/models/*.json
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tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.nii
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tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.tsv
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tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.txt
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tests/dummyData/derivatives/cpp_spm/sub-*/*/*/*.json
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tests/dummyData/derivatives/cpp_spm/sub-*/stats/*/*/*.nii
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tests/*/*.json
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tests/dummyData/derivatives/cpp_spm*/sub-*/
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# ignore content of the build folder of the doc
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docs/build/*

‎.gitmodules

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[submodule "lib/spmup"]
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path = lib/spmup
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url = https://github.com/CPernet/spmup.git
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[submodule "lib/CPP_ROI"]
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path = lib/CPP_ROI
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url = https://github.com/cpp-lln-lab/CPP_ROI.git
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[submodule "lib/slice_display"]
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path = lib/slice_display
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url = https://github.com/bramzandbelt/slice_display.git
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[submodule "lib/brain_colours"]
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path = lib/brain_colours
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url = https://github.com/CPernet/brain_colours.git

‎.travis.yml

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This file was deleted.

‎.zenodo.json

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"affiliation": "Université Catholique de Louvain",
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"name": "Gurtubay, Ane",
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"orcid": "0000-0003-3824-2219"
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},
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},
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{
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"affiliation": "Université Catholique de Louvain",
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"name": "Falagiarda, Federica",
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"orcid": "0000-0001-7844-1605"
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},
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{
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"affiliation": "Université de Montréal",
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"name": "MacLean, Michèle",
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"orcid": "0000-0002-0174-9326"
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}
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],
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"keywords": [
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],
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"license": "GPL-3",
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"upload_type": "software"
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}
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}

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