Clarify license scope and add third-party notices

CITATION.cff

@@ -13,6 +13,7 @@ title: "RABIES: Rodent Automated Bold Improvement of EPI Sequences."
 version: 0.6.1
 date-released: 2026-05-25
 url: "https://github.com/CoBrALab/RABIES"
+license-url: "https://github.com/CoBrALab/RABIES/blob/master/LICENSE"
 
 
 preferred-citation:

Dockerfile

@@ -22,6 +22,10 @@ RUN curl -L -O https://afni.nimh.nih.gov/pub/dist/tgz/linux_ubuntu_16_64.tgz &&
     rm -f linux_ubuntu_16_64.tgz
 ENV PATH=/opt/afni${PATH:+:$PATH}
 
+# record the AFNI build shipped here, so THIRD_PARTY_NOTICES.md can point at the
+# corresponding source (GPLv3 section 6(d))
+RUN (3dDespike -ver 2>&1 | head -1 || echo "unknown") > /AFNI_VERSION && cat /AFNI_VERSION
+
 # Install minc-toolkit
 RUN curl -L --output /tmp/minc-toolkit-1.9.18.deb \
   https://packages.bic.mni.mcgill.ca/minc-toolkit/min/minc-toolkit-1.9.18-20200813-Ubuntu_18.04-x86_64.deb && \
@@ -60,7 +64,7 @@ ENV HOME=/home/$MAMBA_USER
 ENV RABIES=${HOME}/RABIES
 RUN mkdir $RABIES
 
-COPY rabies_environment.yml setup.py MANIFEST.in README.md LICENSE dependencies.txt $RABIES/
+COPY rabies_environment.yml setup.py MANIFEST.in README.md LICENSE THIRD_PARTY_NOTICES.md dependencies.txt $RABIES/
 
 COPY rabies $RABIES/rabies
 COPY minc-toolkit-extras $RABIES/minc-toolkit-extras

LICENSE

@@ -74,3 +74,9 @@ NO WARRANTY
 11. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED ON IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
 
 END OF TERMS AND CONDITIONS
+
+SCOPE
+
+This License applies to the RABIES source code only. Third-party software and
+data distributed with RABIES, including in the container image, remain under
+their own licenses. See THIRD_PARTY_NOTICES.md.

MANIFEST.in

@@ -1 +1,4 @@
-include README.md LICENSE
+include README.md LICENSE THIRD_PARTY_NOTICES.md
+recursive-include rabies *.md
+include minc-toolkit-extras/LICENSE
+include optimized_antsMultivariateTemplateConstruction/LICENSE

README.md

@@ -55,6 +55,8 @@ Simple resting-state connectivity analyses are made available after preprocessin
 ## License
 The [RABIES license](https://github.com/CoBrALab/RABIES/blob/master/LICENSE) allows for uses in academic and educational environments only. Commercial use requires a commercial license from CoBrALab <contact@cobralab.ca>, <http://cobralab.ca>
 
+The RABIES license applies to the RABIES source code only. Third-party software and data distributed with RABIES, including in the container image, remain under their own licenses. See [THIRD_PARTY_NOTICES.md](https://github.com/CoBrALab/RABIES/blob/master/THIRD_PARTY_NOTICES.md).
+
 ## Acknowledgements
 This software was developped by the [CoBrALab](https://cobralab.ca/), located at the Cerebral Imaging Center of the Douglas Mental Health University Institute, Montreal, Canada, in affiliation with McGill University, Montreal, Canada. This work was supported by funding from Healthy Brains, Healthy Lives (HBHL), the Fonds de recherche du Québec - Santé (FRQS) and - Nature et technologies (FRQNT), and the Natural Sciences and Engineering Research Council (NSERC) of Canada. [fMRIPrep](https://fmriprep.org/en/stable/) was an important inspirational source for this project, in particular with regards to best practices for software reproducibility and code design using Nipype. We also thank the organizers of [BrainHack School Montreal](https://school.brainhackmtl.org/), which guided the initial steps of this project in 2018.
 

THIRD_PARTY_NOTICES.md

@@ -0,0 +1,90 @@
+# Third-party notices
+
+The RABIES license (`LICENSE`, Academic Public License) applies to the RABIES
+source code only. RABIES is distributed with third-party software and data that
+remain under their own licenses. Those licenses are listed below.
+
+RABIES starts the external tools below as separate programs. It does not link
+them into its own process. Their presence alongside RABIES on a disk or in a
+container image is aggregation, not combination.
+
+## Corresponding source for GPL components
+
+RABIES conveys the binaries below without changes. The corresponding source is
+available at the locations named. This satisfies GNU GPL version 3 section 6(d).
+
+For the AFNI binaries, RABIES elects version 3 of the GNU General Public
+License, as permitted by the "or later" term on the GPL-licensed files inside
+them. See the AFNI entry below.
+
+| Component | Version | License | Corresponding source |
+|---|---|---|---|
+| AFNI (`3dDespike`, `3dTshift`, `3dWarp`, `3dAutobox`, `libmri.so`, `libf2c.so`) | see `AFNI_VERSION` below | Public domain and CC-BY-4.0, with GPL-2.0-or-later parts | <https://github.com/afni/afni> |
+| MINC Toolkit v2 | 1.9.18-20200813 | GPL-3.0 | <https://github.com/BIC-MNI/minc-toolkit-v2> |
+| GNU parallel | as packaged in Ubuntu 22.04 (jammy) | GPL-3.0-or-later | `apt-get source parallel` on Ubuntu 22.04 |
+| rsync, patch, perl, imagemagick, curl, unzip, gdebi-core | as packaged in Ubuntu 22.04 (jammy) | various, including GPL | `apt-get source <package>` on Ubuntu 22.04 |
+
+The AFNI build in this image is recorded in the file `AFNI_VERSION` at the image
+root. Use that version to select the matching tag or commit in the AFNI
+repository.
+
+Most of AFNI is a United States Government work in the public domain, and the
+portions copyrighted by the Medical College of Wisconsin are under CC-BY-4.0.
+AFNI also bundles files under other licenses. One of them,
+`src/niml/niml_md5.c` (Christophe Devine, GPL-2.0-or-later), is compiled into
+`libmri`, so the AFNI binaries conveyed here are a combined work under
+GPL-2.0-or-later. See <https://github.com/afni/afni/blob/master/LICENSE.txt>.
+
+## FSL
+
+FSL is installed from the FSL conda channel and is **not free for commercial
+use**. The FSL license text is at `/opt/conda/LICENCE.FSL` in the image. The FSL
+source is at `/opt/conda/src/` in the image, as the FSL conda packages ship it.
+For commercial licensing, contact Oxford University Innovation at
+<fsl@innovation.ox.ac.uk>, Reference Project 9564.
+
+## ANTs and other Apache-2.0 components
+
+ANTs 2.5.0, `nipype` and `SimpleITK` are under the Apache License 2.0. A copy of
+that license is at <https://www.apache.org/licenses/LICENSE-2.0>.
+
+## ICA-AROMA
+
+`rabies/confound_correction_pkg/mod_ICA_AROMA/` is a modified copy of ICA-AROMA
+(<https://github.com/maartenmennes/ICA-AROMA>), under the Apache License 2.0.
+The license text is kept alongside the code at
+`rabies/confound_correction_pkg/mod_ICA_AROMA/license.md`. RABIES changes to
+those files are marked with `###RABIES modification` comments.
+
+## Python dependencies
+
+All Python dependencies are under permissive licenses: BSD-3-Clause (numpy,
+scipy, pandas, scikit-learn, scikit-image, seaborn, pathos, traits, networkx),
+MIT (nibabel, pybids, future), Apache-2.0 (nipype, SimpleITK), the Python
+Software Foundation license (matplotlib), MPL-2.0 and MIT (tqdm), and the
+Unlicense (qbatch).
+
+## CoBrALab components
+
+`minc-toolkit-extras` and `optimized_antsMultivariateTemplateConstruction` are
+CoBrALab software under the same Academic Public License as RABIES. Their
+license files are included with them.
+
+## Atlases and data
+
+The DSURQE 40-micron atlas comes from the Mouse Imaging Centre at The Centre for
+Phenogenomics. See <https://www.mouseimaging.ca/>. Cite Dorr et al. 2008,
+Steadman et al. 2014, Ullmann et al. 2013, Richards et al. 2011, Qiu et al.
+2016, and Egan et al. 2015.
+
+Other template and mask files come from Zenodo record 19069284 ("RABIES_extras",
+Gabriel Desrosiers-Gregoire, CoBrALab), under CC-BY-4.0.
+See <https://zenodo.org/records/19069284>.
+
+## The N3 patch
+
+`patch/nu_estimate_np_and_em.diff` changes a file from N3, copyright 1996 John
+G. Sled, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill
+University. That file carries a permissive notice which allows use, copying,
+modification and distribution if the copyright notice stays. The patch keeps the
+notice.

setup.py

@@ -132,7 +132,8 @@ def run(self):
     install_requires=REQUIRED,
     extras_require=EXTRAS,
     include_package_data=True,
-    license='LICENSE',
+    license='Academic Public License',
+    license_files=('LICENSE', 'THIRD_PARTY_NOTICES.md'),
     classifiers=[
         # Trove classifiers
         # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers