COPYING.txt

### Licence FSL ###
FMRIB Software Library, Release 5.0 (c) 2012, The University of Oxford
(the "Software")

The Software remains the property of the University of Oxford ("the
University").

The Software is distributed "AS IS" under this Licence solely for
non-commercial use in the hope that it will be useful, but in order
that the University as a charitable foundation protects its assets for
the benefit of its educational and research purposes, the University
makes clear that no condition is made or to be implied, nor is any
warranty given or to be implied, as to the accuracy of the Software,
or that it will be suitable for any particular purpose or for use
under any specific conditions. Furthermore, the University disclaims
all responsibility for the use which is made of the Software. It
further disclaims any liability for the outcomes arising from using
the Software.

The Licensee agrees to indemnify the University and hold the
University harmless from and against any and all claims, damages and
liabilities asserted by third parties (including claims for
negligence) which arise directly or indirectly from the use of the
Software or the sale of any products based on the Software.

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.

You are not permitted under this Licence to use this Software
commercially. Use for which any financial return is received shall be
defined as commercial use, and includes (1) integration of all or part
of the source code or the Software into a product for sale or license
by or on behalf of Licensee to third parties or (2) use of the
Software or any derivative of it for research with the final aim of
developing software products for sale or license to a third party or
(3) use of the Software or any derivative of it for research with the
final aim of developing non-software products for sale or license to a
third party, or (4) use of the Software to provide any service to an
external organisation for which payment is received. If you are
interested in using the Software commercially, please contact Isis
Innovation Limited ("Isis"), the technology transfer company of the
University, to negotiate a licence. Contact details are:
innovation@isis.ox.ac.uk quoting reference BS/9564.


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The Standard Space Atlases

The Cerebellum, Harvard-Oxford, JHU, Juelich, Striatum and Thalamus atlases, 
whilst not being the property of Oxford, are released under the terms of the
main FSL licence above, at the request of their owners. These atlases
should therefore not be used for commercial purposes; for such
purposes please contact the primary co-ordinator for the relevant
atlas:

Harvard-Oxford: steve@fmrib.ox.ac.uk
JHU: susumu@mri.jhu.edu
Juelich: S.Eickhoff@fz-juelich.de
Thalamus: behrens@fmrib.ox.ac.uk
Cerebellum: j.diedrichsen@bangor.ac.uk
Striatum: andri.tziortzi@gmail.com

### Licence ANTs ###
Copyright (c) 2009-2013 ConsortiumOfANTS
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
  notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
  notice, this list of conditions and the following disclaimer in the
  documentation and/or other materials provided with the distribution.
3. Neither the name of the consortium nor the names of its contributors
  may be used to endorse or promote products derived from this software
  without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE CONSORTIUM AND CONTRIBUTORS ``AS IS'' AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED.  IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE. 

### TrackVis License Agreement ###

The General Hospital Corporation

ACADEMIC RESEARCH END-USER
SOFTWARE LICENSE AGREEMENT

By downloading, using, reproducing, displaying or otherwise accessing the 
Software which is the subject of this Agreement, Licensee (defined below) 
hereby agrees to all of the terms and conditions in this Agreement.  If 
Licensee does not so agree, Licensee shall have no license or right to 
use, reproduce or display the Software.

This Academic Research End-User Software License Agreement (the 
"Agreement") is by and between The General Hospital Corporation, d/b/a 
Massachusetts General Hospital, a Massachusetts not-for-profit 
corporation, with a principal place of business at 55 Fruit Street, 
Boston, Massachusetts 02114 (the "Licensor") and the individual who is 
or has engaged in downloading, using, reproducing, displaying or otherwise 
accessing the Software described herein (the "Individual") and the 
institution or entity which employs or is otherwise affiliated with such 
Individual in connection with the Individual's use of the Software (the 
"Institution" and together with the Individual, collectively 
"Licensee"), and is effective as of the date the Software is first 
downloaded or otherwise accessed by the Individual or the Institution (the 
"Effective Date").  Each party to this Agreement is referred to herein 
as a "Party" and collectively as the "Parties."

RECITALS

Licensor, through its investigators Ruopeng Wang, MS and Van Wedeen, MD of 
the Department of Radiology, has developed the Software (defined below), 
for use in the field of Diffusion Imaging research, and desires to permit 
Licensee to use the software for Research Purposes only (defined below).

Licensee desires to license the Software solely for Research Purposes in 
accordance with the terms and conditions hereof.

         Now therefore, in consideration of the premises and covenants 
hereinafter set forth and other good and valuable consideration, the 
receipt and sufficiency of which is hereby acknowledged, the Parties 
hereby agree as follows:

I.       Certain Definitions.  As used in this Agreement, the following 
terms shall have the following meanings:

         (a)    "Affiliate" with respect to either entity Party means 
any corporation or other legal entity other than that Party in whatever 
country organized, controlling, controlled by or under common control with 
that Party.  The term "control" shall mean the power, direct or 
indirect, to elect or appoint fifty percent (50%) or more of the directors 
or trustees, or to cause direction of management and policies, whether 
through the ownership of voting securities, by contract or otherwise.

        (b)    "Binary Code" means the embodiment of a computer program 
which is not in human-readable form, and which is derived from source code 
of such program by means of assembly or compilation into either a 
computer-specific non-executable code, or an executable code capable of 
being run on a computer system.

        (c)     "Commercial Purposes" shall mean the sale, lease, license or 
other transfer of the Software, use of the Software for the performance of 
contract research, or to produce or manufacture products for sale, or to 
develop, use, and/or distribute educational materials based on the 
Software, including but not limited to courseware or text books.

        (d)     "Patent Rights" means Licensor's rights in the Software 
under U.S. and foreign patent law, if applicable, as may be further 
described in Appendix A.

        (e)     "Research Purposes" means the academic or government 
funded research under the direction of the Individual at the Institution.

        (f)     "Software" means the computer programs known as TrackVis 
and Diffusion Toolkit and any related documentation as further defined and 
described in Appendix A.

2.        Software License Grant.  Subject to the terms and conditions 
contained in this Agreement, Licensor hereby grants to Licensee a 
nonexclusive, nontransferable, nonsublicensable, royalty-free license:

        (i)     under Licensor's copyright rights, to reproduce and display the 
Software; and
        (ii)    under Licensor's Patent Rights, to use the Software (but 
not to sell or otherwise transfer the Software);

provided, however, that the foregoing license grant is limited to Research 
Purposes only and only at the Institution.  The Software shall not be 
reproduced, displayed or used for any Commercial Purposes unless Licensor 
has consented in writing in advance and the Parties have entered into a 
commercial license agreement containing appropriate terms for royalties, 
and such other terms and conditions as are required by Licensor.

3.        Title and Ownership.  The Software is protected by copyright and 
foreign treaties, and may be subject to Patent Rights and other 
proprietary rights of Licensor and, if applicable, its licensor(s). 
Except to the extent of the limited license provided for in this 
Agreement, Licensor shall retain all of its rights, title and interest in 
and to the Software.  This Agreement does not grant any rights in or to 
any intellectual property owned or licensed by Licensor except those 
rights expressly granted hereunder, and except as specifically set forth 
in this Agreement, Licensee shall have no other rights in or to the 
Software nor any underlying intellectual property.

4.        Conditions.  As a condition to the license granted hereunder, 
Licensee, and each of Individual or the Institution, as applicable, shall 
comply at all times with each of the following:

        (a)     Licensee shall preserve and maintain all applicable 
attributions, copyright notices and licenses included in or applicable to 
the Software.

        (b)     Licensee may make copies of the Software but only to the extent 
required to support Licensee's authorized use of the Software for 
Licensee's Research Purposes.  Licensee agrees to reproduce on any such 
copies all of Licensor's proprietary notices contained in and on the 
Software and its associated media.

        (c)     Licensee shall use the Software only for Research Purposes and 
only at the Institution.

        (d)     Licensee shall not sell, license, distribute, rent, lease, 
offer on an ASP or service bureau basis, grant a security interest in, 
sublicense or otherwise transfer or permit any third party (other than 
Licensee's own employees, students and fellows or other collaborators 
solely in connection with permitted activities at the Institution) to 
access or use all or any portion of the Software in any form or any of the 
rights therein or thereto.

        (e)     This Agreement does not grant any rights with respect to 
third party software, except those rights that Licensor has been 
authorized by a third party to grant to Licensee, and accordingly Licensee 
is solely responsible for obtaining any permissions from third parties 
which are necessary to use, reproduce, or display, the Software.

        (f)     Licensee shall exercise its rights pursuant to this Agreement in 
compliance with all applicable governmental laws, regulations and orders, 
including without limitation those relating to export and import control.

        (g)     To the extent such restriction is not prohibited by 
applicable law, Licensee shall not decompile, disassemble or reverse 
engineer the Software or its structure, sequence, organization, algorithms 
or data.

        (h)     Licensee shall notify Licensor promptly if it becomes 
aware of any unauthorized access to or use or transfer of the Software.

        (i)     Institution shall be jointly responsible for the actions of 
Individuals hereunder with respect to the Software and compliance with the 
terms of this Agreement.   Licensee hereby represents and warrants that 
all information provided to Licensor in connection with accessing, 
downloading and/or using the Software is accurate, true and complete.

5.        Limitations.

(a)        LICENSEE ACKNOWLEDGES THAT THE SOFTWARE HAS BEEN DESIGNED FOR 
RESEARCH PURPOSES ONLY AND HAS NOT BEEN REVIEWED OR APPROVED BY THE FOOD 
AND DRUG ADMINISTRATION OR BY ANY OTHER AGENCY, AND FURTHER ACKNOWLEDGES 
THAT CLINICAL APPLICATIONS ARE NEITHER RECOMMENDED NOR ADVISED.

(b)        Licensee shall be solely responsible for installing and 
maintaining the Software and for testing the Software for proper 
operation.  Unless otherwise agreed in writing, Licensor shall have no 
obligation to provide to Licensee any support, maintenance, corrections, 
debugging, improvements, modifications, upgrades or updates of the 
Software, or otherwise assist Licensee in installing, configuring, 
integrating, understanding or using the Software.

6.        Publication.  Licensee may publish and present the results of 
Licensee's use of the Software in peer-reviewed journals.  Licensee 
agrees to provide acknowledgement to Licensor and its designated 
professional staff, Ruopeng Wang, MS and Van Wedeen, MD, who participated 
in the creation of the Software, in such publications or presentations in 
accordance with standard academic practice.

7.        Term and Termination.  This Agreement and the license granted by 
Licensor hereunder shall commence on the Effective Date and continue in 
effect until terminated by any Party as provided herein.  Licensee may 
terminate this Agreement at any time by destroying all copies of the 
Software and notifying Licensor in writing of such destruction, or 
returning all copies of the Software to Licensor.  Licensor may terminate 
this Agreement upon sixty (60) days prior notice to Licensee if Licensee 
does not comply with any of the material provisions of this Agreement and 
such breach remains uncured at the end of such sixty (60) day period, 
provided however that in the case of any breach of this Agreement that 
Licensor in its reasonable judgment deems uncurable, Licensor may 
terminate this Agreement immediately upon notification to Licensee.  Upon 
any such termination, Licensee shall immediately cease all uses of the 
Software and any portion thereof, and shall return or destroy all copies 
of the Software and any portion thereof and, if so requested, provide 
written certification of such destruction to Licensor.

8.        Disclaimer.  Licensee accepts the Software free of charge and on 
an "AS IS" basis.  Licensee understands and acknowledges that the Software 
is experimental, may contain errors and is subject to further development 
and revision and assumes the entire risk as to its use of the Software. 
Licensor does not guarantee the accuracy of the Software, or of any 
results or data, and assumes no obligation to notify Licensee of any bug 
fixes, enhancements or other modifications that may be made to the 
Software.  LICENSOR SPECIFICALLY DISCLAIMS ALL EXPRESS AND IMPLIED 
WARRANTIES OF ANY KIND INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF 
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT.

9.        Limitation of Liability; Indemnification.  IN NO EVENT SHALL 
LICENSOR OR ANY OF ITS TRUSTEES, DIRECTORS, OFFICERS, MEDICAL OR 
PROFESSIONAL STAFF, EMPLOYEES, STUDENTS OR  AGENTS ("LICENSOR'S 
PERSONNEL") BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
INCIDENTAL, EXEMPLARY OR CONSEQUENTIAL DAMAGES HOWEVER CAUSED AND ON ANY 
THEORY OF LIABILITY ARISING IN ANY WAY RELATED TO THE SOFTWARE OR THIS 
AGREEMENT, EVEN IF LICENSOR OR ANY OF LICENSOR'S PERSONNEL HAS BEEN 
ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.  EXCEPT TO THE EXTENT 
PROHIBITED BY LAW OR REGULATION, LICENSEE ASSUMES ALL LIABILITY FOR 
LICENSEE'S USE, REPRODUCTION,  AND DISPLAY OF THE SOFTWARE, AND AGREES TO 
INDEMNIFY AND HOLD HARMLESS LICENSOR AND EACH OF LICENSOR'S PERSONNEL 
FROM AND AGAINST ANY AND ALL DAMAGES, COSTS, LIABILITY, LOSS OR EXPENSES 
(INCLUDING ATTORNEYS' FEES AND COSTS) ARISING IN CONNECTION WITH ANY 
CLAIMS, SUITS, ACTIONS, DEMANDS AND JUDGMENTS RELATED TO LICENSEE'S USE, 
REPRODUCTION,  AND DISPLAY OF THE SOFTWARE.

10.        Independent Status.  Neither the making of this Agreement nor the 
performance of its provisions shall be construed to constitute any Party 
an agent, employee or legal representative of the other Party for any 
purpose whatsoever.

11.        Use of Name.  Except as expressly provided in this Agreement or 
pursuant to specific prior written permission of the applicable party, 
Licensee shall not use any of the names, logos or trademarks, or any 
adaptation thereof, of Licensor or any of its Affiliates, or of any 
trustee, director, officer, staff member, employee, student or agent 
thereof, or of any funding agency, in any advertising, promotional or 
sales material or publicity or in any document employed to obtain funds or 
financing, or to endorse or promote research results or products produced 
in whole or in part by operation of the Software or derived from or based 
on the Software.  Such permission shall be obtained from Licensor's Chief 
Public Affairs Officer.  Licensee hereby grants permission to Licensor to 
use Licensee's name for purposes of obtaining funds from any funding 
agency.

12.        U.S. Government Rights.  For Software supported by federal 
funding, the license granted under this Agreement is subject to the 
rights, conditions and limitations imposed by U.S. law including without 
limitation 35 U.S.C. § 202 et seq. and regulations pertaining thereto. 
Notwithstanding the foregoing, the license granted under this Agreement 
does not constitute a response by Licensee to any request for proposals, 
bid solicitation or other invitation or offer to contract by any 
governmental authority but instead constitutes an offer to enter into a 
license agreement only upon the terms set forth herein.  If the U.S. 
Government or any other governmental authority shall seek to acquire the 
Software and its acquisition of such Software would result in the U.S. 
Government or such other governmental authority having rights in the 
Software that are at variance with the terms and conditions of this 
Agreement and license, Licensee shall not be bound by any such rights 
unless it shall have expressly entered into an amendment of this Agreement 
that shall set forth such rights in accordance with any applicable 
governmental rules or regulations, including the Federal Acquisition 
Regulation and the Defense Federal Acquisition Regulation Supplement.

13.        General.  This Agreement constitutes the entire understanding of 
the Parties with respect to the subject matter hereof, superseding and 
merging any prior oral or written understandings between the Parties with 
respect thereto.  Sections 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 and 13 shall 
survive any termination of this Agreement.  This Agreement may be modified 
or amended only in a writing signed by duly authorized representatives of 
the Parties hereto.  If any part of this Agreement is adjudged to be 
invalid or unenforceable, the Parties intend that such invalidity shall 
not affect any other provision hereof.  Any waiver or failure of any Party 
to assert a right hereunder shall not constitute a waiver or excuse a 
similar failure in any other circumstance.  Licensee shall not assign any 
of its rights or obligations under this Agreement without the prior 
written consent of Licensor.  Except to the extent prohibited by law or 
regulation, this Agreement shall be governed by and construed in 
accordance with the laws of The Commonwealth of Massachusetts, excluding 
its provisions with respect to conflict of laws, and each Party consents 
to the exclusive jurisdiction and venue of courts in Boston, Massachusetts 
in all disputes relating to this Agreement.  Headings in this Agreement 
are for convenience only and are not intended to be used to interpret or 
construe this Agreement.  This Agreement may be executed in counterparts 
and delivered by facsimile with the same effect as an original.  Each of 
the undersigned represents that such individual is duly authorized to 
execute this Agreement.



Appendix A

Description of the Software

1.        Diffusion Toolkit in binary code form:  Diffusion Toolkit is a 
software tool for the performance of data reconstruction and fiber 
tracking for diffusion MR imaging, utilizing but not limited to tensor 
data, diffusion spectrum imaging (DSI), high angular resolution diffusion 
imaging (HARDI) data and Q-ball imaging data.

2.        TrackVis in binary code form: TrackVis is a 3-dimensional 
visualization program that allows real-time visualization and analysis of 
the fiber track data that was created by Diffusion Toolkit.