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‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at [email protected]. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
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[homepage]: http://contributor-covenant.org
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[version]: http://contributor-covenant.org/version/1/4/

‎CONTRIBUTING.md

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# Contributing to `nipype_tutorial`
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Welcome to the `nipype_tutorial` repository! We're excited you're here and want to contribute.
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These guidelines are designed to make it as easy as possible to get involved.
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If you have any questions that aren't discussed below, please let us know by opening an [issue][link_issues]!
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Before you start you'll need to set up a free [GitHub][link_github] account and sign in.
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Here are some [instructions][link_signupinstructions] on how to do just that!
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### Labels
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The current list of labels are [here][link_labels] and include:
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* [![Help Wanted](https://img.shields.io/badge/-help%20wanted-159818.svg)][link_helpwanted]
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*These issues contain a task that a member of the team has determined we need additional help with.*
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If you feel that you can contribute to one of these issues, we especially encourage you to do so!
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* [![Bug](https://img.shields.io/badge/-bug-fc2929.svg)][link_bugs]
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*These issues point to problems in the project.*
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If you find new a bug, please give as much detail as possible in your issue, including steps to recreate the error.
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If you experience the same bug as one already listed, please add any additional information that you have as a comment.
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* [![Enhancement](https://img.shields.io/badge/-enhancement-84b6eb.svg)][link_feature]
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*These issues are asking for enhancements to be added to the project.*
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Please try to make sure that your requested feature is distinct from any others that have already been requested or implemented.
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If you find one that's similar but there are subtle differences please reference the other request in your issue.
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## Making a change
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We appreciate all contributions to `nipype_tutorial`, but those accepted fastest will follow a workflow similar to the following:
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**1. Comment on an existing issue or open a new issue referencing your addition.**
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This allows other members of the `nipype_tutorial` development team to confirm that you aren't overlapping with work that's currently underway and that everyone is on the same page with the goal of the work you're going to carry out.
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[This blog][link_pushpullblog] is a nice explanation of why putting this work in up front is so useful to everyone involved.
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**2. [Fork][link_fork] the [`nipype_tutorial` repository][link_nipype_tutorial] to your profile.**
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This is now your own unique copy of `nipype_tutorial`.
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Changes here won't effect anyone else's work, so it's a safe space to explore edits to the code!
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Make sure to [keep your fork up to date][link_updateupstreamwiki] with the original repository.
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**3. Make the changes you've discussed.**
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Try to keep the changes focused.
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If you feel tempted to "branch out" then please make a [new branch][link_branches].
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**4. Submit a [pull request][link_pullrequest].**
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A member of the development team will review your changes to confirm that they can be merged into the main codebase.
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## Recognizing contributions
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We welcome and recognize all contributions from documentation to testing to code development.
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You can see a list of our current contributors in the [contributors tab][link_contributors].
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## Thank you!
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You're awesome. :wave::smiley:
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<br>
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*&mdash; Based on contributing guidelines from the [STEMMRoleModels][link_stemmrolemodels] project.*
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[link_github]: https://github.com/
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[link_nipype_tutorial]: https://github.com/rmarkello/nipype_tutorial
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[link_signupinstructions]: https://help.github.com/articles/signing-up-for-a-new-github-account
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[link_react]: https://github.com/blog/2119-add-reactions-to-pull-requests-issues-and-comments
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[link_issues]: https://github.com/rmarkello/nipype_tutorial/issues
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[link_labels]: https://github.com/rmarkello/nipype_tutorial/labels
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[link_discussingissues]: https://help.github.com/articles/discussing-projects-in-issues-and-pull-requests
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[link_bugs]: https://github.com/rmarkello/nipype_tutorial/labels/bug
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[link_helpwanted]: https://github.com/rmarkello/nipype_tutorial/labels/help%20wanted
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[link_feature]: https://github.com/rmarkello/nipype_tutorial/labels/enhancement
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[link_pullrequest]: https://help.github.com/articles/creating-a-pull-request/
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[link_fork]: https://help.github.com/articles/fork-a-repo/
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[link_pushpullblog]: https://www.igvita.com/2011/12/19/dont-push-your-pull-requests/
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[link_branches]: https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/
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[link_updateupstreamwiki]: https://help.github.com/articles/syncing-a-fork/
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[link_contributors]: https://github.com/rmarkello/nipype_tutorial/graphs/contributors
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[link_stemmrolemodels]: https://github.com/KirstieJane/STEMMRoleModels

‎Dockerfile

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@@ -63,9 +63,11 @@ RUN apt-get update -qq \
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RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
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ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib"
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ENV FORCE_SPMMCR="1" \
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LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2018b/v95/runtime/glnxa64:/opt/matlabmcr-2018b/v95/bin/glnxa64:/opt/matlabmcr-2018b/v95/sys/os/glnxa64:/opt/matlabmcr-2018b/v95/extern/bin/glnxa64" \
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MATLABCMD="/opt/matlabmcr-2018b/v95/toolbox/matlab"
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LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
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MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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bc \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& echo "Downloading MATLAB Compiler Runtime ..." \
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&& curl -fsSL --retry 5 -o /tmp/mcr.zip https://ssd.mathworks.com/supportfiles/downloads/R2018b/deployment_files/R2018b/installers/glnxa64/MCR_R2018b_glnxa64_installer.zip \
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&& unzip -q /tmp/mcr.zip -d /tmp/mcrtmp \
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&& /tmp/mcrtmp/install -destinationFolder /opt/matlabmcr-2018b -mode silent -agreeToLicense yes \
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&& curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
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&& dpkg -i /tmp/toinstall.deb \
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&& rm /tmp/toinstall.deb \
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&& apt-get install -f \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& curl -fsSL --retry 5 -o /tmp/MCRInstaller.bin https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
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&& chmod +x /tmp/MCRInstaller.bin \
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&& /tmp/MCRInstaller.bin -silent -P installLocation="/opt/matlabmcr-2010a" \
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&& rm -rf /tmp/* \
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&& echo "Downloading standalone SPM ..." \
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&& curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2018b.zip \
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&& curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip \
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&& unzip -q /tmp/spm12.zip -d /tmp \
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&& mkdir -p /opt/spm12-dev \
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&& mv /tmp/spm12/* /opt/spm12-dev/ \
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&& chmod -R 777 /opt/spm12-dev \
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&& mkdir -p /opt/spm12-r7219 \
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&& mv /tmp/spm12/* /opt/spm12-r7219/ \
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&& chmod -R 777 /opt/spm12-r7219 \
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&& rm -rf /tmp/* \
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&& /opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 quit \
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&& sed -i '$iexport SPMMCRCMD=\"/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 script\"' $ND_ENTRYPOINT
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&& /opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
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&& sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
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\n ], \
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\n [ \
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\n "env", \
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\n { \
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\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib" \
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\n } \
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\n ], \
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\n [ \
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\n "spm12", \
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\n { \
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\n "version": "r7219" \
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\n ], \
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‎Singularity

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unzip -q /tmp/mcr.zip -d /tmp/mcrtmp
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/tmp/mcrtmp/install -destinationFolder /opt/matlabmcr-2018b -mode silent -agreeToLicense yes
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curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb
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dpkg -i /tmp/toinstall.deb
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rm /tmp/toinstall.deb
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apt-get install -f
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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curl -fsSL --retry 5 -o /tmp/MCRInstaller.bin https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin
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chmod +x /tmp/MCRInstaller.bin
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/tmp/MCRInstaller.bin -silent -P installLocation="/opt/matlabmcr-2010a"
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curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2018b.zip
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curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip
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mkdir -p /opt/spm12-dev
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chmod -R 777 /opt/spm12-dev
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mkdir -p /opt/spm12-r7219
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mv /tmp/spm12/* /opt/spm12-r7219/
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chmod -R 777 /opt/spm12-r7219
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/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 quit
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sed -i '$iexport SPMMCRCMD=\"/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 script\"' $ND_ENTRYPOINT
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/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit
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sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
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\n "env",
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\n {
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\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib"
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\n }
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\n ],
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\n [
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\n "spm12",
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\n {
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\n "version": "r7219"
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\n ],
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\n [
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export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib"
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export FORCE_SPMMCR="1"
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export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2018b/v95/runtime/glnxa64:/opt/matlabmcr-2018b/v95/bin/glnxa64:/opt/matlabmcr-2018b/v95/sys/os/glnxa64:/opt/matlabmcr-2018b/v95/extern/bin/glnxa64"
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export MATLABCMD="/opt/matlabmcr-2018b/v95/toolbox/matlab"
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export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64"
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export MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
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export CONDA_DIR="/opt/miniconda-latest"
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export PATH="/opt/miniconda-latest/bin:$PATH"
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‎generate.sh

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git-annex-standalone vim emacs-nox nano less ncdu \
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tig git-annex-remote-rclone octave netbase \
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--add-to-entrypoint "source /etc/fsl/fsl.sh" \
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--spm12 version=dev \
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--env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib" \
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--spm12 version=r7219 \
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--user=neuro \
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--miniconda miniconda_version="4.3.31" \
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conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
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--spm12 version=dev \
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--env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib" \
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--spm12 version=r7219 \
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--user=neuro \
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--miniconda miniconda_version="4.3.31" \
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conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions

‎notebooks/advanced_spmmcr.ipynb

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"outputs": [],
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"source": [
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"from nipype.interfaces import spm\n",
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"matlab_cmd = '/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95/ script'\n",
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"matlab_cmd = '/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713/ script'\n",
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"spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)"
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]
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},

‎notebooks/basic_debug.ipynb

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" config.enable_debug_mode()\n",
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" ```\n",
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"\n",
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" as the first import of your nipype script. To enable debug logging use:\n",
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"\n",
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" ```python\n",
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" from nipype import logging\n",
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" logging.update_logging(config)\n",
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" ```\n",
24+
" as the first import of your nipype script.\n",
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" \n",
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" **Note:**\n",
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" - Turning on debug will rerun your workflows and will rerun them after debugging is turned off.\n",
28+
" - Turning on debug mode will also override log levels specified elsewhere, such as in the nipype configuration. \n",
29+
" - `workflow`, `interface` and `utils` loggers will all be set to level `DEBUG`.\n",
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" \n",
31-
" **Note:** Turning on debug will rerun your workflows and will rerun them after debugging is turned off.\n",
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"\n",
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"- There are several configuration options that can help with debugging.\n",
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" See [Configuration File](config_file.ipynb) for more details:\n",

‎notebooks/basic_error_and_crashes.ipynb

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"\n",
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"```python\n",
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"from nipype.interfaces.matlab import MatlabCommand\n",
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"MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')\n",
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"MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')\n",
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"```"
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]
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},

‎notebooks/basic_execution_configuration.ipynb

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"metadata": {},
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"outputs": [],
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"source": [
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"from nipype import config, logging\n",
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"config.enable_debug_mode()\n",
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"logging.update_logging(config)"
279+
"from nipype import config\n",
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"config.enable_debug_mode()"
282281
]
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},
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{
@@ -296,8 +295,23 @@
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"source": [
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"config.set('execution', 'stop_on_first_crash', 'true')\n",
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"config.set('execution', 'remove_unnecessary_outputs', 'false')\n",
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"config.set('execution', 'keep_inputs', 'true')\n",
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"config.set('logging', 'workflow_level', 'DEBUG')\n",
300-
"config.set('logging', 'interface_level', 'DEBUG')"
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"config.set('logging', 'interface_level', 'DEBUG')\n",
301+
"config.set('logging', 'utils_level', 'DEBUG')"
302+
]
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},
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{
305+
"cell_type": "markdown",
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"metadata": {},
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"source": [
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"The primary loggers (`workflow`, `interface` and `utils`) are also reset to level `DEBUG`.\n",
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"\n",
310+
"You may wish to adjust these manually using:\n",
311+
"```python\n",
312+
"from nipype import logging\n",
313+
"logging.getLogger(<logger>).setLevel(<level>)\n",
314+
"```"
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]
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},
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{

‎notebooks/basic_interfaces.ipynb

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Perfect! Exactly what we want. Hmm... what else could we want from BET? Well, it's actually a fairly complicated program. As is the case for all FSL binaries, just call it with no arguments to see all its options."
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"Perfect! Exactly what we want. Hmm... what else could we want from BET? Well, it's actually a fairly complicated program. As is the case for all FSL binaries, just call it with the help flag `-h` to see all its options."
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]
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},
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{

‎notebooks/example_normalize.ipynb

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@@ -351,7 +351,7 @@
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"# Smoothing withds used during preprocessing\n",
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"fwhm = [4, 8]\n",
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"\n",
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"template = '/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'"
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"template = '/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'"
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]
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},
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{

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