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.azure-pipelines/windows.yml

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parameters:
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name: ''
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vmImage: ''
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matrix: []
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jobs:
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- job: ${{ parameters.name }}
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pool:
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vmImage: ${{ parameters.vmImage }}
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variables:
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EXTRA_WHEELS: "https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
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strategy:
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matrix:
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${{ insert }}: ${{ parameters.matrix }}
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steps:
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- task: UsePythonVersion@0
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inputs:
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versionSpec: '$(PYTHON_VERSION)'
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addToPath: true
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architecture: '$(PYTHON_ARCH)'
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- script: |
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python -m pip install --upgrade pip setuptools>=30.3.0 wheel
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displayName: 'Update build tools'
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- script: |
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python -m pip install --find-links %EXTRA_WHEELS% numpy scipy matplotlib h5py pydicom
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python -m pip install nose mock coverage codecov
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displayName: 'Install dependencies'
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- script: |
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python -m pip install .
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SET NIBABEL_DATA_DIR=%CD%\\nibabel-data
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displayName: 'Install nibabel'
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- script: |
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mkdir for_testing
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cd for_testing
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cp ../.coveragerc .
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nosetests --with-doctest --with-coverage --cover-package nibabel nibabel
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displayName: 'Nose tests'
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- script: |
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cd for_testing
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codecov
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displayName: 'Upload To Codecov'
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env:
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CODECOV_TOKEN: $(CODECOV_TOKEN)

.coveragerc

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*/externals/*
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*/benchmarks/*
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*/tests/*
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nibabel/_version.py

.gitattributes

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nibabel/COMMIT_INFO.txt export-subst
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nibabel/_version.py export-subst

.github/CODE_OF_CONDUCT.md

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# Community Guidelines
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Nibabel is a [NIPY](https://nipy.org) project, and we strive to adhere to the
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[NIPY Community Code](https://nipy.org/conduct.html), reproduced below.
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The NIPY community is a community of practice devoted to the use of the Python programming language
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in the analysis of neuroimaging data. The following code of conduct is a guideline for our behavior
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as we participate in this community.
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It is based on, and heavily inspired by a reading of the Python community code of conduct, the
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Apache foundation code of conduct, the Debian code of conduct, and the Ten Principles of Burning
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Man.
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## The code of conduct for the NIPY community
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The Neuroimaging in Python (NIPY) community is made up of members with a diverse set of skills,
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personalities, background, and experiences. We welcome these differences because they are the
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source of diverse ideas, solutions and decisions about our work. Decisions we make affect users,
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colleagues, and through scientific results, the general public. We take these consequences
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seriously when making decisions. When you are working with members of the community, we encourage
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you to follow these guidelines, which help steer our interactions and help keep NIPY a positive,
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successful, and growing community.
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### A member of the NIPY community is:
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#### Open
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Members of the community are open to collaboration. Be it on the reuse of data, on the
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implementation of methods, on finding technical solutions, establishing best practices, and
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otherwise. We are accepting of all who wish to take part in our activities, fostering an
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environment where anyone can participate and everyone can make a difference.
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#### Be collaborative!
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Our work will be used by other people, and in turn we will depend on the work of others. When we
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make something for the benefit of others, we are willing to explain to others how it works, so that
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they can build on the work to make it even better. We are willing to provide constructive criticism
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on the work of others and accept criticism of our own work, as the experiences and skill sets of
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other members contribute to the whole of our efforts.
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#### Be inquisitive!
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Nobody knows everything! Asking questions early avoids many problems later, so questions are
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encouraged, though they may be directed to the appropriate forum. Those who are asked should be
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responsive and helpful, within the context of our shared goal of improving neuroimaging practice.
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#### Considerate
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Members of the community are considerate of their peers. We are thoughtful when addressing the
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efforts of others, keeping in mind that often-times the labor was completed simply for the good of
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the community. We are attentive in our communications, whether in person or online, and we are
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tactful when approaching differing views.
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#### Be careful in the words that you choose:
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We value courtesy, kindness and inclusiveness in all our interactions. Therefore, we take
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responsibility for our own speech. In particular, we avoid:
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* Personal insults.
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* Violent threats or language directed against another person.
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* Sexist, racist, or otherwise discriminatory jokes and language.
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* Any form of sexual or violent material.
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* Sharing private content, such as emails sent privately or non-publicly, or unlogged forums such
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as IRC channel history.
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* Excessive or unnecessary profanity.
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* Repeated harassment of others. In general, if someone asks you to stop, then stop.
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* Advocating for, or encouraging, any of the above behaviour.
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#### Try to be concise in communication
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Keep in mind that what you write once will be read by many others. Writing a short email means
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people can understand the conversation as efficiently as possible. Even short emails should always
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strive to be empathetic, welcoming, friendly and patient. When a long explanation is necessary,
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consider adding a summary.
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Try to bring new ideas to a conversation, so that each message adds something unique to the
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conversation. Keep in mind that, when using email, the rest of the thread still contains the other
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messages with arguments that have already been made.
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Try to stay on topic, especially in discussions that are already fairly long and complex.
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#### Respectful
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Members of the community are respectful. We are respectful of others, their positions, their
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skills, their commitments, and their efforts. We are respectful of the volunteer and professional
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efforts that permeate the NIPY community. We are respectful of the processes set forth in the
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community, and we work within them. When we disagree, we are courteous and kind in raising our
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issues.
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## Incident Reporting
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We put great value on respectful, friendly and helpful communication.
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If you feel that any of our Nibabel communications lack respect, or are unfriendly or unhelpful,
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please try the following steps:
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* If you feel able, please let the person who has sent the email or comment that you found it
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disrespectful / unhelpful / unfriendly, and why;
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* If you don't feel able to do that, or that didn't work, please contact Chris Markiewicz directly
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by email (<markiewicz@stanford.edu>), and he will do his best to resolve it.
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If you don't feel comfortable contacting Chris, please email Matthew Brett
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(<matthew.brett@gmail.com>) instead.
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## Attribution
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The vast majority of the above was taken from the NIPY Code of Conduct.

.github/CONTRIBUTING.md

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# Contributing to NiBabel
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Welcome to the NiBabel repository!
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We're excited you're here and want to contribute.
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Please see the [NiBabel Developer Guidelines][link_devguide] on our
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on our [documentation website][link_docs].
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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 in our documentation, or it's
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difficult to find what you're looking for, please let us know by opening an
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[issue][link_issues]!
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[link_docs]: https://nipy.org/nibabel
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[link_devguide]: https://nipy.org/nibabel/devel/devguide.html
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[link_issues]: https://github.com/poldracklab/fmriprep/issues

.gitmodules

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url = git://github.com/matthew-brett/nitest-minc2.git
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[submodule "nipy-ecattest"]
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path = nibabel-data/nipy-ecattest
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url = https://github.com/freec84/nipy-ecattest
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url = https://github.com/effigies/nipy-ecattest
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[submodule "nibabel-data/nitest-freesurfer"]
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path = nibabel-data/nitest-freesurfer
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url = https://bitbucket.org/nipy/nitest-freesurfer.git

.mailmap

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#
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# This file is up-to-date if the command git log --format="%aN <%aE>" | sort -u
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# gives no duplicates.
10-
Michael Hanke <michael.hanke@gmail.com> <mhanke-guest@82381867-18eb-0310-98a2-9474e637aba2>
11-
Michael Hanke <michael.hanke@gmail.com> <michaelhanke@mvpa1.dartmouth.edu>
12-
Yaroslav Halchenko <debian@onerussian.com> <yoh-guest@82381867-18eb-0310-98a2-9474e637aba2>
10+
Alexandre Gramfort <alexandre.gramfort@inria.fr> Alexandre Gramfort <alexandre.gramfort@m4x.org>
11+
Ariel Rokem <arokem@gmail.com> arokem <arokem@gmail.com>
12+
B. Nolan Nichols <nolan.nichols@gmail.com> Nolan Nichols <nolan.nichols@gmail.com>
13+
Basile Pinsard <basile.pinsard@gmail.com> bpinsard <basile.pinsard@gmail.com>
14+
Basile Pinsard <basile.pinsard@gmail.com> bpinsard <bpinsard@imed.jussieu.fr>
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Ben Cipollini <ben.cipollini@gmail.com> Ben Cipollini <bcipolli@ucsd.edu>
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Bertrand Thirion <bertrand.thirion@inria.fr> bthirion <bertrand.thirion@inria.fr>
14-
Stephan Gerhard <git@unidesign.ch> Stephan Gerhard <git@github.com>
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Christian Haselgrove <christian.haselgrove@umassmed.edu> Christian Haselgrove <Christian.Haselgrove@umassmed.edu>
18+
Christopher J. Markiewicz <markiewicz@stanford.edu> Chris Johnson <effigies@bu.edu>
19+
Christopher J. Markiewicz <markiewicz@stanford.edu> Chris Markiewicz <effigies@gmail.com>
20+
Christopher J. Markiewicz <markiewicz@stanford.edu> Chris Markiewicz <markiewicz@stanford.edu>
21+
Christopher J. Markiewicz <markiewicz@stanford.edu> Christopher J. Markiewicz <effigies@bu.edu>
22+
Christopher J. Markiewicz <markiewicz@stanford.edu> Christopher J. Markiewicz <effigies@gmail.com>
1623
Cindee Madison <cindee@berkeley.edu> CindeeM <cindee@berkeley.edu>
1724
Cindee Madison <cindee@berkeley.edu> cindeem <cindee@berkeley.edu>
18-
Ian Nimmo-Smith <iannimmosmith@gmail.com> Ian Nimmo-Smith <ian.nimmo-smith@mrc-cbu.cam.ac.uk>
19-
Jean-Baptiste Poline <jbpoline@gmail.com> jbpoline <jbpoline@gmail.com>
25+
Demian Wassermann <demian@bwh.harvard.edu> Demian Wassermann <demian.wassermann@inria.fr>
26+
Dimitri Papadopoulos Orfanos <dimitri.papadopoulos@cea.fr> Dimitri Papadopoulos <DimitriPapadopoulos@users.noreply.github.com>
27+
Eric Larson <larson.eric.d@gmail.com> Eric89GXL <larson.eric.d@gmail.com>
28+
Eric Larson <larson.eric.d@gmail.com> larsoner <larson.eric.d@gmail.com>
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Fernando Pérez-García <fepegar@gmail.com> Fernando <fepegar@gmail.com>
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Félix C. Morency <felix.morency@gmail.com> Felix C. Morency <felix.c.morency@usherbrooke.ca>
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Félix C. Morency <felix.morency@gmail.com> Félix C. Morency <felix.c.morency@usherbrooke.ca>
22-
Krish Subramaniam <krish.subramaniam@gmail.com> Krish Subramaniam <krish@monster.nmr.mgh.harvard.edu>
23-
Eric Larson <larson.eric.d@gmail.com> Eric89GXL <larson.eric.d@gmail.com>
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Alexandre Gramfort <alexandre.gramfort@inria.fr> Alexandre Gramfort <alexandre.gramfort@m4x.org>
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Gael Varoquaux <gael.varoquaux@normalesup.org> GaelVaroquaux <gael.varoquaux@normalesup.org>
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Kevin S. Hahn <kevinshahn@gmail.com> Kevin S. Hahn <kshahn@stanford.edu>
27-
Basile Pinsard <basile.pinsard@gmail.com> bpinsard <basile.pinsard@gmail.com>
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Basile Pinsard <basile.pinsard@gmail.com> bpinsard <bpinsard@imed.jussieu.fr>
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Nguyen, Ly <nguyen60@seattleu.edu> lxn2 <lxn2@uw.edu>
30-
Ben Cipollini <ben.cipollini@gmail.com> Ben Cipollini <bcipolli@ucsd.edu>
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Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <markiewicz@stanford.edu>
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Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@bu.edu>
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Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@gmail.com>
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Chris Markiewicz <effigies@gmail.com> Chris Johnson <effigies@bu.edu>
33+
Gregory R. Lee <grlee77@gmail.com> Gregory R. Lee <gregory.lee@cchmc.org>
34+
Ian Nimmo-Smith <iannimmosmith@gmail.com> Ian Nimmo-Smith <ian.nimmo-smith@mrc-cbu.cam.ac.uk>
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Jaakko Leppäkangas <jaeilepp@student.jyu.fi> jaeilepp <jaeilepp@student.jyu.fi>
36-
Ariel Rokem <arokem@gmail.com> arokem <arokem@gmail.com>
37-
Oliver P. Hinds <ohinds@gmail.com> ohinds <ohinds@gmail.com>
38-
Marc-Alexandre Côté <marc.cote.19@gmail.com> Marc-Alexandre Cote <marc.cote.19@gmail.com>
39-
Satrajit Ghosh <satra@mit.edu> Satrajit Ghosh <satrajit.ghosh@gmail.com>
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Jasper J.F. van den Bosch <japsai@gmail.com> Jasper <japsai@gmail.com>
41-
Gregory R. Lee <grlee77@gmail.com> Gregory R. Lee <gregory.lee@cchmc.org>
42-
Demian Wassermann <demian@bwh.harvard.edu> Demian Wassermann <demian.wassermann@inria.fr>
37+
Jean-Baptiste Poline <jbpoline@gmail.com> jbpoline <jbpoline@gmail.com>
38+
Jon Haitz Legarreta <jon.haitz.legarreta@gmail.com> Jon Haitz Legarreta Gorroño <jon.haitz.legarreta@gmail.com>
39+
Kesshi Jordan <Kesshi.Jordan@ucsf.edu> kesshijordan <Kesshi.Jordan@ucsf.edu>
40+
Kevin S. Hahn <kevinshahn@gmail.com> Kevin S. Hahn <kshahn@stanford.edu>
41+
Konstantinos Raktivan <constracti@gmail.com> constracti <constracti@gmail.com>
42+
Krish Subramaniam <krish.subramaniam@gmail.com> Krish Subramaniam <krish@monster.nmr.mgh.harvard.edu>
43+
Marc-Alexandre Côté <marc.cote.19@gmail.com> Marc-Alexandre Cote <marc.cote.19@gmail.com>
44+
Mathias Goncalves <mathiasg@mit.edu> mathiasg <mathiasg@mit.edu>
45+
Matthew Cieslak <mattcieslak@gmail.com> Matt Cieslak <mattcieslak@gmail.com>
46+
Michael Hanke <michael.hanke@gmail.com> <mhanke-guest@82381867-18eb-0310-98a2-9474e637aba2>
47+
Michael Hanke <michael.hanke@gmail.com> <michaelhanke@mvpa1.dartmouth.edu>
48+
Michiel Cottaar <MichielCottaar@protonmail.com> Michiel Cottaar <MichielCottaar@protonmail.ch>
49+
Ly Nguyen <nguyen60@seattleu.edu> lxn2 <lxn2@uw.edu>
50+
Oliver P. Hinds <ohinds@gmail.com> ohinds <ohinds@gmail.com>
4351
Paul McCarthy <pauldmccarthy@gmail.com> Paul McCarthy <pauld.mccarthy@gmail.com>
52+
Satrajit Ghosh <satra@mit.edu> Satrajit Ghosh <satrajit.ghosh@gmail.com>
53+
Serge Koudoro <skab12@gmail.com> skoudoro <skab12@gmail.com>
54+
Stephan Gerhard <git@unidesign.ch> Stephan Gerhard <git@github.com>
55+
Thomas Roos <thomasroos@live.nl> Roosted7 <thomasroos@live.nl>
56+
Venkateswara Reddy Reddam <R3DDY97@users.noreply.github.com> R3DDY97 <R3DDY97@users.noreply.github.com>
57+
Yaroslav O. Halchenko <debian@onerussian.com> <yoh-guest@82381867-18eb-0310-98a2-9474e637aba2>
58+
Yaroslav O. Halchenko <debian@onerussian.com> Yaroslav Halchenko <debian@onerussian.com>

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