NITRC: CMIG Pipeline: Agreement Page

License Agreement

By downloading this file you agree to the following (if you do not agree to this, please press "Cancel" below):

The CMIG Pipeline is shared as a package containing multiple components:

A. Executable Docker and Singularity image files

B. Miscellaneous scripts and configuration files

C. Miscellaneous libraries

D. Brain atlas image files

E. Gradient nonlinearity field correction files

F. Publicly available and/or redistributable software

a. AFNI

b. DCMTK

c. dcm2niix

d. FreeSurfer

e. FSL

f. GNU Scientific Library

g. Intel CCE

h. Intel MKL

i. SPM

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A. Executable Docker and Singularity image files

Docker image files: images/*.tar

e.g.,

images/cmig_pipeline_abcd_dicom-mmps_271b.tar

images/cmig_test-mmps_271b.tar

Singularity image files: images/*.sif

e.g.,

images/cmig_pipeline_abcd_dicom-mmps_271b.sif

images/cmig_test-mmps_271b.sif

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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B. Miscellaneous scripts, configuration files

classify

scripts

pubsw/bin

pubsw/packages/MMPS/MMPS_271/bin

pubsw/packages/MMPS/MMPS_271/csh

pubsw/packages/MMPS/MMPS_271/parms

pubsw/packages/MMPS/MMPS_271/python

pubsw/packages/MMPS/MMPS_271/setup

pubsw/packages/MMPS/MMPS_271/sh

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

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C. Miscellaneous libraries

pubsw/packages/MMPS/MMPS_271/lib/BasicStructs

pubsw/packages/MMPS/MMPS_271/lib/Interpolation

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

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D. Brain atlas image files

pubsw/packages/MMPS/MMPS_271/atlases/DTI_Atlas

pubsw/packages/MMPS/MMPS_271/atlases/DTI_ROI_Dispersion

pubsw/packages/MMPS/MMPS_271/atlases/FA_Atlas

pubsw/packages/MMPS/MMPS_271/atlases/T1T2

pubsw/packages/MMPS/MMPS_271/atlases/T1_Atlas

pubsw/packages/MMPS/MMPS_271/atlases/T2_Atlas

pubsw/packages/MMPS/MMPS_271/atlases/fuzzy_clusters

Atlas brain image files are provided under the terms of the Creative Commons Attribution-NonCommercial 4.0 International license (CC-BY-NC 4.0).

https://creativecommons.org/licenses/by-nc/4.0

see: documentation/licenses/CC-BY-NC-4.0.txt

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E. Gradient nonlinearity field correction files

pubsw/packages/MMPS/MMPS_271/external/matlab/Projects/MorphometryToolbox/6_DistortionCorrection/gradient_nonlinearity/gradient_data

Gradient warping field data files are provided under the terms of the Creative Commons Attribution-NonCommercial 4.0 International license (CC-BY-NC 4.0).

https://creativecommons.org/licenses/by-nc/4.0

see: documentation/licenses/CC-BY-NC-4.0.txt

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F. Publicly available and/or redistributable software

These publicly available and/or redistributable software packages are provided without warranty of any kind and are redistributed under the terms of the respective licenses for each package. For more information, refer to the information below and the files compiled in the documentation/license directory.

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AFNI: pubsw/packages/afni/AFNI_2010_10_19_1028/

https://afni.nimh.nih.gov/Legal_info

AFNI is distributed freely under the GNU General Public License.

see: documentation/licenses/AFNI_README.copyright

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DCMTK: pubsw/packages/dcmtk/3.6.0/

https://dicom.offis.de/download/dcmtk/current/COPYRIGHT

see: documentation/licenses/DCMTK_COPYRIGHT

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dcm2niix: pubsw/packages/MMPS/MMPS_271/external/bin/dcm2niix

https://github.com/rordenlab/dcm2niix/releases

dcm2niix is a binary executable distributed under the BSD license

see: documentation/licenses/dcm2niix_license.txt

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FreeSurfer: pubsw/packages/freesurfer/RH4-x86_64-R530/

pubsw/packages/freesurfer/RH4-x86_64-R711/

https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense

NOTE: FreeSurfer users should obtain a free FreeSurfer license file

https://surfer.nmr.mgh.harvard.edu/regis...

Copy the license file to the freesurfer software directory; e.g.,

cp license.txt ~/cmig_docker/pubsw/packages/freesurfer/RH4-x86_64-R711

see: documentation/licenses/FreeSurfer_530_LICENSE

documentation/licenses/FreeSurfer_711/

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FSL: pubsw/packages/fsl/fsl-5.0.2.2-centos6_64/

https://fsl.fmrib.ox.ac.uk/fsl/docs/#/license

No part of the Software may be reproduced, modified, transmitted or transferred in any form or by any means, electronic or mechanical, without the express permission of the University. The permission of the University is not required if the said reproduction, modification, transmission or transference is done without financial return, the conditions of this Licence are imposed upon the receiver of the product, and all original and amended source code is included in any transmitted product. You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions.

see: documentation/licenses/FSL_LICENSE

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GNU Scientific Library: pubsw/packages/MMPS/MMPS_271/lib/gsl

https://www.gnu.org/software/gsl/

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.

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Intel CCE: pubsw/packages/opt/intel/cce/

Intel (R) ++ Compiler 10.1 for Linux

http://www.intel.com/software/products

see: documentation/licenses/intel_cce_README.txt

documentation/licenses/intel_cce_clicense

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Intel MKL: pubsw/packages/opt/intel/mkl/

The Intel(R) Math Kernel Library (Intel(R) MKL)

www.intel.com/software/products/mkl

see: documentation/licenses/intel_mkl_Readme.txt

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SPM: pubsw/packages/spm/spm5b/

pubsw/packages/spm/mods/mmil_spm_dicom_headers.m

https://www.fil.ion.ucl.ac.uk/spm/software

https://github.com/spm/spm/blob/main/LICENCE

spm is licensed under the GNU General Public License v2.0.

If you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights.

mmil_spm_dicom_headers.m file is a modified version of spm_dicom_headers.m and is shared in accordance with the GNU General Public License v2.0.

see: documentation/licenses/spm_LICENSE.man

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