Licensing and Derived Works¶

The NiPreps community believes that software is an integral component of scientific practice, and that any scientific claim must be verifiable by following the chain of reasoning from observation to conclusion. To achieve this, software must be free to use, inspect, and critique. We also believe that you should be free to modify our software to improve it or adapt it to new use cases.

As software development is a dynamic process, code modifications can quickly become confusing as the original and modified versions depart from each other. For the sake of transparency and verification, when you modify our code, we ask that you document both the version of the software that you started with and the changes you make.

We believe these freedoms are best promoted by distributing our software under free/open source software licenses, and the license we feel best promotes these goals is the Apache License, Version 2.0.

This page outlines our commitment to transparent development and our expectations for developers who adapt NiPreps code to use in other projects.

Licensing of NiPreps projects¶

All software packages and tools under the NiPreps umbrella must be licensed under the Apache License 2.0 by default, unless otherwise stated. The authors of new NiPreps packages may not abide by this general rule of thumb if necessary and/or sufficiently justified (e.g., the source code is actually derived from a product licensed under a copyleft license).

Containerized Images bundling NiPreps components and their dependencies can be distributed under a free and open-source license without copyleft, such as the MIT License. In such a case, the attribution notice of the MIT license must be present in the header comment of the container image bootstraping file (for instance, the so-called Dockerfile). This different licensing must be also indicated in the NOTICE file of the corresponding NiPreps components bundled within the image.

Docker-wrappers such as the fmriprep-docker package may be licensed under any free and open-source license without copyleft, such as the MIT License. This different licensing must be also indicated in the NOTICE file of the corresponding NiPreps components bundled within the image.

Data (distributed within the test data of packages or through the nipreps-data GitHub organization) will preferably be distributed under the Creative Commons Zero v1.0 Universal.

Under no circumstances any NiPreps software or data will be made publicly available unlicensed. If you find any component of NiPreps that is unlicensed, please make us aware at nipreps@gmail.com at your earliest convenience.

The Apache License 2.0¶

(This section is adapted from this blog post by D. Marín)

The Apache License was created by the Apache Software Foundation (ASF) as the license for its Apache HTTP Server.

Just as the MIT License, it’s a very permissive non-copyleft license that allows using the software for any purpose, distributing it, modifying it, and distributing derived works of it without concern for royalties. Its main differences, compared to the MIT License, are:

Using the Apache License, the authors of the software grant patent licenses to any user or distributor of the code. This patent licenses apply to any patent that, being licenseable by any of the software author, would be infringed by the piece of code they have created.
Apache License required that unmodified parts in derived works keep the License.
In every licensed file, any original copyright, patent, trademark or attribution notices must be preserved.
In every licensed file change, there must be a notification stating that changes have been made in the file.
If the Apache-licensed software includes a NOTICE file, this file and its contents must be preserved in all the derived works.
If anyone intentionally sends a contribution for an Apache-licensed software to its authors, this contribution can automatically be used under the Apache License.

This license is interesting because of the automatic patent license, and the clause about contribution submission.

It’s compatible with the GPL, so you can mix Apache licensed-code into GPL software.

Why Apache-2.0?¶

In the case of scientific software, we believe that clearly stating that a Derived Work introduces changes into the original Work is a fundamental measure of transparency. Other than that, we wanted a permissive, non-copyleft license.

What is our expectation for Derived Works?¶

At the bare minimum, you must meet the conditions of the license (simplified version) about preserving the license text and copyright/attribution notices as well as corresponding statements of changes.

How to state that a file has been changed in a Derived Work. We suggest the following steps, heavily influenced by P. Ombredanne's recommendations at StackExchange:

In each source file, add a note to the header comment stating that the file has been modified, with an approximate date, and a high-level description of the changes. The date and the description of the changes are not strictly required, but they are positive etiquette from a software engineering standpoint and substantially improve the transparency of the changes from a scientific point of view.
If the source file did not have a license notice in the header comment, please add it to avoid ambiguity.
Deleted files: please keep the file with just the header comment and state that the file is deleted. The change statement should follow the suggestion in 1), preferably stating whether the source has been deleted or moved over to other files. If preserving the filename as-is might become confusing to the user of the Derived Work, the filename can be modified to be marked as hidden with a dot . or underscore _ prefix, or modifying the extension.
Preferably, also include a link to the original file in our GitHub repository, making sure the link is done to a particular commit state.

What changes would we like to see annotated? The high-level description of the changes will preferably contain:

Correction of bugs
Substantial performance improvement decisions
Replacement of relevant methods and dependencies by alternatives
Changes to the license

Example of our expectations¶

Let's say a Derived Work modifies the sdcflows.viz.utils code-base. The file may or may not have the attribution notice. At the time of writing, the header comment of this file is:

Header comment in the original Work

With attribution notice

# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Visualization tooling."""

Without attribution notice

# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Visualization tooling."""

Either way (whether the attribution notice is present or not), we suggest to update this header comment to something along the lines of the following:

Suggested header comment in the Derived Work

Required

# <shebang and editor settings can be preserved or removed freely>
#
# <your attribution notice, either maintaining the Apache-2.0 license or changing the license>
#
# STATEMENT OF CHANGES: This file is derived from sources licensed under the Apache-2.0 terms,
# and this file has been changed.
# The original file this work derives from is found at:
# https://github.com/nipreps/sdcflows/blob/50393a8584dd0abf5f8e16e6ba66c43e1126f844/sdcflows/viz/utils.py
#
# [April 2021] CHANGES:
#    * BUGFIX: Outdated function call from the ``svgutils`` dependency that changed API as of version 0.3.2.
#    * ENH: Changed plotting dependency to the new `netplotbrain` package.
#    * DOC: Added docstrings to some functions that lacked them.
#
# ORIGINAL WORK'S ATTRIBUTION NOTICE:
#
#     Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
#
#     Licensed under the Apache License, Version 2.0 (the "License");
#     you may not use this file except in compliance with the License.
#     You may obtain a copy of the License at
#
#         http://www.apache.org/licenses/LICENSE-2.0
#
#     Unless required by applicable law or agreed to in writing, software
#     distributed under the License is distributed on an "AS IS" BASIS,
#     WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#     See the License for the specific language governing permissions and
#     limitations under the License.
"""Visualization tooling."""

The lines highlighted with yellow color are explicitly required by the Apache-2.0 conditions.

Recommended (commit)

# <shebang and editor settings can be preserved or removed freely>
#
# <your attribution notice, either maintaining the Apache-2.0 license or changing the license>
#
# STATEMENT OF CHANGES: This file is derived from sources licensed under the Apache-2.0 terms,
# and this file has been changed.
# The original file this work derives from is found at:
# https://github.com/nipreps/sdcflows/blob/50393a8584dd0abf5f8e16e6ba66c43e1126f844/sdcflows/viz/utils.py
#
# [April 2021] CHANGES:
#    * BUGFIX: Outdated function call from the ``svgutils`` dependency that changed API as of version 0.3.2.
#    * ENH: Changed plotting dependency to the new `netplotbrain` package.
#    * DOC: Added docstrings to some functions that lacked them.
#
# ORIGINAL WORK'S ATTRIBUTION NOTICE:
#
#     Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
#
#     Licensed under the Apache License, Version 2.0 (the "License");
#     you may not use this file except in compliance with the License.
#     You may obtain a copy of the License at
#
#         http://www.apache.org/licenses/LICENSE-2.0
#
#     Unless required by applicable law or agreed to in writing, software
#     distributed under the License is distributed on an "AS IS" BASIS,
#     WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#     See the License for the specific language governing permissions and
#     limitations under the License.
"""Visualization tooling."""

The lines highlighted with green color are recommended by the NiPreps Developers.

Recommended (version)

# <shebang and editor settings can be preserved or removed freely>
#
# <your attribution notice, either maintaining the Apache-2.0 license or changing the license>
#
# STATEMENT OF CHANGES: This file is derived from sources licensed under the Apache-2.0 terms,
# and this file has been changed.
# The original file this work derives from is found within
# the version 2.0.2 distribution of the software.
#
# [April 2021] CHANGES:
#    * BUGFIX: Outdated function call from the ``svgutils`` dependency that changed API as of version 0.3.2.
#    * ENH: Changed plotting dependency to the new `netplotbrain` package.
#    * DOC: Added docstrings to some functions that lacked them.
#
# ORIGINAL WORK'S ATTRIBUTION NOTICE:
#
#     Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
#
#     Licensed under the Apache License, Version 2.0 (the "License");
#     you may not use this file except in compliance with the License.
#     You may obtain a copy of the License at
#
#         http://www.apache.org/licenses/LICENSE-2.0
#
#     Unless required by applicable law or agreed to in writing, software
#     distributed under the License is distributed on an "AS IS" BASIS,
#     WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#     See the License for the specific language governing permissions and
#     limitations under the License.
"""Visualization tooling."""

The lines highlighted with green color are recommended by the NiPreps Developers.

Although it is not mandated by the license letter, the spirit of the Apache-2.0 (and all other licenses stipulating the statement of changes, such as the CC-BY 4.0) suggests that a date of modification and an overview of outstanding changes are pertinent. We also suggest a link to the original code, including the commit-hash (that long string starting with 50393a in the URL above) for the location of the exact origin of the file. Alternatively, Derived Works may point to a exact release identifier where the original file is part of the code-base distribution. Please make sure to remove or replace with appropriate contents the comment tags <...> above.

What if a Derived Work does not modify this particular file? You should retain the original attribution notice as is (or introduce it if missing), unless you are relicensing the file. In that case, proceed with the suggestions above, and note the license change in the STATEMENT OF CHANGES block of the header comment.

Are papers using Apache-2.0 licensed software considered as Derived Works?¶

No, they don't because they only reuse the software (in other words, they don't redistribute the software). The license stipulates that redistribution must retain the license and attribution notices as they are. In the scientific context, it is likely that a particular tool is modified (for example, to replace a method that you think is not appropriate for your data). Then, redistribution of the source would be desirable from the transparent reporting point of view, and therefore you should honor the License.

Generally, works using our NiPreps just need to follow the citation guidelines of the particular project and report the citation boilerplate including all software versions and literature references in the closest letter possible to that generated by the tool.

Licensing of Docker and Singularity images¶

Container images redistribute copies of NiPreps alongside their third-party dependencies, all of them bundled in the image. If the applicable license is Apache-2.0, then the text of a NOTICE file must be shown to the user. All NiPreps must insert a NOTICE file into their containerized distributions and print its contents out in the command line output, as well as in the visual reports. This NOTICE file for containers will be placed in the /.docker/NOTICE path of the repository, and this file must replace the /NOTICE file (if it exists) at image building time. Alternatively, and if the corresponding NiPreps Developers consider that the Apache-2.0 imposes too onerous requirements for the container image distribution, the source code of such images (e.g., Dockerfile) can be licensed under the MIT license.

Example NOTICE file for fMRIPrep

Python distribution /NOTICE

fMRIPrep
Copyright 2021 The NiPreps Developers.

This product includes software developed by
the NiPreps Community (https://nipreps.org/).

Portions of this software were developed at the Department of
Psychology at Stanford University, Stanford, CA, US.

This software contains code ultimately derived from the epidewarp.fsl
script (https://www.nmr.mgh.harvard.edu/~greve/fbirn/b0/epidewarp.fsl)
by Doug Greve, Dave Tuch, Tom Liu, and Bryon Mueller with generous
help from the FSL crew (www.fmrib.ox.ac.uk/fsl) and the Biomedical
Informatics Research Network (www.nbirn.net).

Container image distribution /.docker/NOTICE

fMRIPrep Container Image distribution
Copyright 2021 The NiPreps Developers.

This product includes fMRIPrep and software developed by
the NiPreps Community (https://nipreps.org/).

Portions of this software were developed at the Department of
Psychology at Stanford University, Stanford, CA, US.

This product bundles AFNI <version-placeholder>, which is available under
the Gnu General Public License.
Major portions of AFNI were written at the Medical College of Wisconsin,
which owns the copyright to that code. For fuller details, see
http://afni.nimh.nih.gov/pub/dist/src/README.copyright.

This product bundles ANTs <version-placeholder>, which is available under
the BSD 3-clause license terms.
Copyright 2009-2013 ConsortiumOfANTS.

This product bundles BIDS-Validator <version-placeholder>, which is available
under the MIT License.
Copyright 2015 The Board of Trustees of the Leland Stanford Junior University.

This product bundles the Connectome Workbench <version-placeholder>, which
is available under the GPL-v2
(https://www.humanconnectome.org/software/connectome-workbench-license).

This product bundles FSL <version-placeholder>, which is available
under a custom license with commercial restrictions
(https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence).
Copyright 2018, The University of Oxford.

This product bundles FreeSurfer <version-placeholder>, which is available
under a custom license and requires obtaining a license key
(https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense).
Copyright 2011, The General Hospital Corporation, Boston MA, USA.

This product bundles code derived from ICA-AROMA, both (fork and original work)
are available under the Apache-2.0 license.
(https://github.com/oesteban/ICA-AROMA/blob/master/license.md)
Copyright 2021, Maarten Mennes

This product bundles Miniconda <version-placeholder>, which is available
under a BSD 3-clause license.
(c) 2017 Continuum Analytics, Inc. (dba Anaconda, Inc.).
https://www.anaconda.com. All Rights Reserved

This product bundles NeuroDebian, which adheres to the
Debian Free Software Guidelines (DFSG)
https://www.debian.org/social_contract#guidelines
and the terms of the Debian Social Contract version 1.1.

This product bundles tools by the NiPy community, such as NiBabel
(MIT License, https://github.com/nipy/nibabel/blob/master/COPYING),
and NiPype (Apache-2.0, https://github.com/nipy/nipype/blob/master/LICENSE).

This product bundles Pandoc <version-placeholder>, which is available
under the GPL version 2 or later.
Copyright (C) 2006-2021 John MacFarlane <jgm at berkeley dot edu>

This product bundles SVGO <version-placeholder>, which is available
under the MIT License.
Copyright (c) Kir Belevich

This product bundles tedana <version-placeholder>, which is available under
the GNU Lesser General Public License v2.1.
Copyright 2018, tedana developers.

TemplateFlow, a component of this bundle, contains neuroimaging template
and atlas data under several permissive licenses.
Please refer to the metadata of the particular template used in your study to
determine the exact terms of the license and how to acknowledge attribution
of those works.

sMRIPrep, a component of this bundle, contains code ultimately derived from
ANTs <version-placeholder>, which is available under
the BSD 3-clause license terms.
Copyright 2009-2013 ConsortiumOfANTS.

sMRIPrep, a component of this bundle, contains code ultimately derived from
Mindboggle <version-placeholder>, which is available under
the Apache License 2.0.
Copyright 2016, Mindboggle team (http://mindboggle.info)

fMRIPrep contains code ultimately derived from the epidewarp.fsl
script (https://www.nmr.mgh.harvard.edu/~greve/fbirn/b0/epidewarp.fsl)
by Doug Greve, Dave Tuch, Tom Liu, and Bryon Mueller with generous
help from the FSL crew (www.fmrib.ox.ac.uk/fsl) and the Biomedical
Informatics Research Network (www.nbirn.net).