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Merge pull request #1478 from softmatterlab/develop
Release 2.0.0.a1
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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: bug
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior:
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1. Go to '...'
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2. Click on '....'
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3. Scroll down to '....'
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4. See error
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Screenshots**
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If applicable, add screenshots to help explain your problem.
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**Desktop (please complete the following information):**
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- OS: [e.g. iOS]
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- Browser [e.g. chrome, safari]
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- Version [e.g. 22]
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**Smartphone (please complete the following information):**
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- Device: [e.g. iPhone6]
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- OS: [e.g. iOS8.1]
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- Browser [e.g. stock browser, safari]
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- Version [e.g. 22]
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**Additional context**
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: enhancement
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.

‎.gitignore‎

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*.asv
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*.asv
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.DS_Store
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braph2/
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Tmp/

‎.zenodo.json‎

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{
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"creators": [
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{
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"orcid": "0000-0001-5057-1846",
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"affiliation": "Gothenburg University",
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"name": "Volpe, Giovanni"
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},
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{
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"orcid": "0000-0002-5388-7712",
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"affiliation": "Gothenburg University",
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"name": "Gómez-Ruiz, Emiliano"
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},
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{
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"orcid": "0000-0001-9598-2278",
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"affiliation": "Gothenburg University",
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"name": "Chang, Yu-Wei"
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},
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{
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"orcid": "0000-0002-4604-2711",
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"affiliation": "Karolinksa Institute",
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"name": "Pereira, Joana"
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},
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{
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"orcid": "0000-0001-7460-741X",
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"affiliation": "Karolinksa Institute",
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"name": "Canal-Garcia, Anna"
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},
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{
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"orcid": "0000-0002-9844-4413",
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"affiliation": "Karolinksa Institute",
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"name": "Mijalkov, Mite"
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},
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{
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"orcid": "0000-0003-2077-5252",
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"affiliation": "Karolinksa Institute",
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"name": "Véreb, Dániel"
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},
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{
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"orcid": "0000-0002-3115-2977",
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"affiliation": "Karolinksa Institute",
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"name": "Westman, Eric"
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}
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],
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"title": "BRAPH 2: Brain Analysis Using Graph Theory 2",
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"related_identifiers": [
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{
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"scheme": "doi",
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"identifier": "10.1371/journal.pone.0178798",
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"relation": "isDocumentedBy",
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"resource_type": "publication-article"
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}
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],
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"description": "An object-oriented software that provides pipelines for conventional brain connectivity analysis as well as more advanced methods, including multilayer networks and deep learning methods." ,
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"keywords": ["Brain", "Software", "Graph", "Multigraph", "Multiplex Graph", "MATLAB", "Neuroimaging", "Deep Learning"],
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"upload_type": "software",
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"communities": [
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{"identifier": "www.braph.org"},
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{"identifier": "https://github.com/softmatterlab/BRAPH-2-Matlab"}
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]
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}

‎CITATION.cff‎

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# This CITATION.cff file was generated with cffinit.
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# Visit https://bit.ly/cffinit to generate yours today!
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cff-version: 1.2.0
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title: 'BRAPH 2: Brain Analysis using Graph Theory 2'
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message: >-
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If you use this software, please cite it using the
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metadata from this file.
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type: software
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authors:
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- given-names: Giovanni
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family-names: Volpe
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email: giovanni.vole@physics.gu.se
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affiliation: Gothenburg University
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orcid: 'https://orcid.org/0000-0001-5057-1846'
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- given-names: Joana
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name-particle: B.
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family-names: Pereira
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email: joana.pereira@ki.se
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affiliation: Karolinska Institute
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orcid: 'https://orcid.org/0000-0002-4604-2711'
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- given-names: Pablo Emiliano
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family-names: Gómez Ruiz
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email: emiliano.gomez@physics.gu.se
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affiliation: Gothenburg University
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orcid: 'https://orcid.org/0000-0002-5388-7712'
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- given-names: Anna
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family-names: Canal-Garcia
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email: anna.canal@ki.se
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affiliation: Karolinska Institute
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orcid: 'https://orcid.org/0000-0001-7460-741X'
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- given-names: Yu-Wei
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family-names: Chang
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email: yu-wei.chang@physics.gu.se
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affiliation: Gothenburg University
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orcid: 'https://orcid.org/0000-0001-9598-2278'
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- given-names: Mite
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family-names: Mijalkov
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email: mite.mijalkov@ki.se
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affiliation: Karolinksa Institute
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orcid: 'https://orcid.org/0000-0002-9844-4413'
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- given-names: Dániel
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family-names: Véreb
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email: daniel.vereb@ki.se
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affiliation: Karolinska Institute
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orcid: 'https://orcid.org/0000-0003-2077-5252'

‎LICENSE‎

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BRAPH Software License Terms
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1 General
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1.1 The Braph software is developed by Prof. Giovanni Volpe (the “Licensor”, “we” or “us”) and related
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contributors as further set forth on the Braph website located at www.braph.org. By installing and
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using Braph, you and your organisation is granted a license to use Braph subject to these terms. If
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you do not accept these terms, please do not install and do not use Braph.
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1.2 This license pertains solely to use of Braph in combination with Matlab® and requires that that
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you also have a proper and valid license to use Matlab® in addition to this license.
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1.3 Braph is provided together with its source code and intended to be viewed and used as open source.
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The intent is that you shall be able to freely use and develop Braph for your research, development
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and educational purposes. However, as much as we encourage use and development of Braph, we want to
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restrict redistribution and commercial sublicensing, which means that there are some restrictions to
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your use set forth in Section 2.4.
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2 Intellectual property rights and license
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2.1 Any and all intellectual property rights, including without limitation copyright protected
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materials, source code, database rights, registered and unregistered trade-marks, registered and
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unregistered design rights, patents and patentable inventions, know how (regardless if patentable or
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not) and all other rights in or relating to Braph is the exclusive property of the Licensor, or the
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property of the Licensor’s contributing licensors as applicable.
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2.2 You are granted a non-exclusive, royalty-free right and license to use Braph for your internal
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research and development, including commercial research and development, as well as for educational
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and academic purposes. The license furthermore includes the right to access and amend the source code
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of Braph and implement such changes in Braph as you deem fit.
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2.3 Any amendments made by you to Braph are your intellectual property that you may use freely as long
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as such use is not contrary to these terms. We encourage that you share amendments with us, in which
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case we are given the right (but not the obligation) to include them in future versions of Braph and
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make them available on these terms or terms materially similar, but you are (i) not required to share
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such amendments and (ii) your amendments if shared are subject to the same limitations of liability
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as set forth in clause 3.
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2.4 Unless you have our prior written consent (which consent may be subject to further terms), you
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are expressly not permitted to re-distribute Braph, amended or in its original form, or any part
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thereof, regardless if such re-distribution is made for free or for a fee. You can however point
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third parties to download Braph directly from our website www.braph.org or other official sources.
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Furthermore, you may not integrate Braph or parts thereof into other software regardless if such
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software is licensed on open source or so called “proprietary” terms. Use contrary to this clause 2.4
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shall in addition render your license to use Braph null and void.
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3 Limitation of liability
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3.1 BRAPH IS PROVIDED “AS IS” AND “WHERE IS” WITHOUT ANY WARRANTY OF ANY KIND, INCLUDING WITHOUT
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LIMITATION ANY IMPLIED, EXPRESS OR STATUTORY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ANY
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WARRANTIES OF FUNCTIONALITY, COMPLETENESS OR ACCURACY, FITNESS FOR A PARTICULAR PURPOSE,
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MERCHANTABILITY, LACK OF VIRUSES OR FREEDOM FROM INFRINGEMENT. FURTHERMORE, YOU ACKNOWLEDGE THAT THE
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SOFTWARE IS NOT, AND WILL NOT BE, ERROR FREE AND RUN WITHOUT ANY INTERRUPTION.
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3.2 We do not accept any liability of any kind, whether direct or indirect, in tort or under any form
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of contractual liability or other doctrine for any damage or claim that may arise as a result of your
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use of Braph, regardless if such use is with our version without any amendment to Braph that you may
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have made.
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3.3 Furthermore, if any third party makes a claim against us as a result of your amended or unamended
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use of Braph, you shall indemnify and hold us harmless from any such claim, including related cost and
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expense such as legal fees.
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4 Attribution
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When publishing scientific results or research reports where Braph has been used in such research, we
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encourage and appreciate that you include references to your use of Braph in such research, as well
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as the scientific publications cited on www.braph.org.
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5 Choice of law, disputes
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These terms shall be governed and construed in accordance with the substantive laws of Sweden, without
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regard to its conflicts of law principles. Any dispute, controversy or claim arising out of or in
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connection with this Agreement, or the breach, termination or invalidity thereof, shall be settled by
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the courts of Sweden with the district court of Stockholm as first instance.
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‎README.md‎

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# Braph-2.0-Matlab
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<p align="center">
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<img width="350" src=https://github.com/softmatterlab/BRAPH-2-Matlab/blob/develop/braph2genesis/src/util/braph2icon.png>
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</p>
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<h3 align="center">Brain Analysis using Graph Theory.</h3>
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<p align="center">
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<a href="https://twitter.com/braph2software" alt="tweeter"><img src="https://img.shields.io/twitter/url?label=BRAPH%202&style=social&url=https%3A%2F%2Ftwitter.com%2Fbraph2software"></a>
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<a href="http://braph.org/" alt="website"><img src="https://img.shields.io/website?up_message=braph.org&url=http%3A%2F%2Fbraph.org%2F"></a>
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<a href="https://doi.org/10.1371/journal.pone.0178798" alt="DOI"><img src="https://img.shields.io/badge/DOI-10.1371%2Fjournal.pone.0178798-blue">
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</a>
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</p>
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<p align="center">
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<a href="#installation">Installation</a> •
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<a href="#braph-2-usage-examples">Examples</a> •
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<a href="#cite-us">Cite us</a> •
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<a href="https://github.com/softmatterlab/BRAPH-2-Matlab/blob/develop/LICENSE">License</a>
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</p>
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An object-oriented software that provides pipelines for conventional brain connectivity analysis as well as more advanced methods, including multilayer networks and deep learning methods.
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# Installation
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BRAPH 2 requires at least **MATLAB R2021a**. BRAPH 2 requires both **Statistics and Machine Learning Toolbox** and **Parallel Computing Toolbox**. For deep learning analysis, **Deep Learning Toolbox** and **Deep Learning Toolbox Converter for ONNX Model Format** are also needed.
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To install BRAPH 2, first download BRAPH 2.
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From our GitHub repository, you can find the latest stable version in the branch <a href="https://github.com/softmatterlab/BRAPH-2-Matlab/tree/master">master</a> and the latest development version in the branch <a href="https://github.com/softmatterlab/BRAPH-2-Matlab/tree/develop">develop</a>.
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You can also download BRAPH 2 from our <a href="http://braph.org/software/braph-2/">website</a>.
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After unzipping the downloaded file into the desired directory and launching MATLAB, change the current folder to **braph2genesis** and run *braph2genesis* (you may have to add it to the path). This installation takes around 5 minutes.
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The installation will be only needed once.
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You can also follow the <a href="http://braph.org/software/braph-2/">Installation</a> section from our website.
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# BRAPH 2 usage examples
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BRAPH 2 is a powerful tool that transforms scripts to pipelines. We provide example data in order to test the different analyses and comparisons from the provided pipelines. Please check the <a href="http://braph.org/tutorials/">Tutorials</a> section from our website for the step-by-step instructions and more details.
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# Cite us!
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If you use BRAPH 2 in your project, please cite us here:
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```
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Emiliano Gomez-Ruiz, Anna Canal-Garcia, Yu-Wei Chang, Daniel Vereb,
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Eric Westman, Mite Mijalkov, Joana Pereira, Giovanni Volpe
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BRAPH 2: A software for brain connectivity analysis
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with multilayer graphs and deep learning.
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```
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See also:
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<https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178798>:
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```
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Mite Mijalkov, Ehsan Kakaei, Joana B Pereira, Eric Westman, Giovanni Volpe
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BRAPH: A graph theory software for the analysis of brain connectivity.
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PLOS ONE 12, e0178798 (2017).
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```

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