MIT License

Copyright © 2016-2020 ARAMIS Lab, http://aramislab.fr/

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.

Several files present in Clinica came from other projects with a specific
LICENSE file that is included below.

The following file is copyright of Rolls ET, Joliot M & Tzourio-Mazoyer N
(2015) . NeuroImage 10.1016/j.neuroimage.2015.07.075:
- clinica/resources/atlases/atlas-AAL2_dseg.nii.gz
The details of license are included below.


The following file is copyright of Joliot M, Jobard G, Naveau M, Delcroix N,
Petit L, Zago L, Crivello F, Mellet E, Mazoyer B & Tzourio-Mazoyer N (2015) .
Journal of Neuroscience Methods 10.1016/j.jneumeth.2015.07.013:
- clinica/resources/atlases/atlas-AICHA_dseg.nii.gz
The details of license are included below.


The following files based on Alexander Hammers' brain atlas, made available for
the Euripides project, Nov 2009 (A):
- clinica/resources/atlases/atlas-Hammers_dseg.tsv
- clinica/resources/atlases/atlas-Hammers_dseg.nii.gz
The details of license are included below.


The following files are copyright of Shattuck DW, Mirza M, Adisetiyo V,
Hojatkashani C, Salamon G, Narr KL, Poldrack RA, Bilder RM, Toga AW (2008)
Construction of a 3D Probabilistic Atlas of Human Cortical Structures,
NeuroImage 39 (3): 1064-1070. DOI:	10.1016/j.neuroimage.2007.09.031:
- clinica/resources/atlases/atlas-LPBA40_dseg.tsv
- clinica/resources/atlases/atlas-LPBA40_dseg.nii.gz
The details of license are included below.


The following files derived from the ``MICCAI 2012 Grand Challenge and Workshop
on Multi-Atlas Labeling''
(https://masi.vuse.vanderbilt.edu/workshop2012/index.php/Challenge_Details).
These data were released under the Creative Commons Attribution-NonCommercial
(CC BY-NC) with no end date. Users should credit the MRI scans as originating
from the OASIS project (http://www.oasis-brains.org/) and the labeled data as
"provided by Neuromorphometrics, Inc. (http://Neuromorphometrics.com/) under
academic subscription".  These references should be included in all workshop
and final publications:
- clinica/resources/atlases/atlas-Neuromorphometrics_dseg.tsv
- clinica/resources/atlases/atlas-Neuromorphometrics_dseg.nii.gz
The details of license are included below.

The clinica/lib/clinicasurfstat/SurfStat library is Copyright 2003 K.J. Worsley.
The details of license are included below.


The following files are copyright of Tzourio-Mazoyer N, Landeau B,
Papathanassiou D, Crivello F, Etard O, Delcroix N, Mazoyer B, Joliot M.
Automated anatomical labeling of activations in SPM using a macroscopic
anatomical parcellation of the MNI MRI single-subject brain. Neuroimage. 2002
Jan;15(1):273-89.PUBMED ID: 11771995.
    clinica/resources/mask_cerebellum+pons_eroded_6mm.nii.gz
    clinica/resources/mask_pons_eroded_6mm.nii.gz
The software used to produce those files is the WFU PickAtlas Standard Atlases:
Maldjian JA, Laurienti PJ, Kraft RA, Burdette JH. An automated method for
neuroanatomic and cytoarchitectonic atlas-based interrogation of fMRI data
sets. Neuroimage. 2003 Jul;19(3):1233-9.
PUBMED ID: 12880848
Maldjian JA, Laurienti PJ, Burdette JH. Precentral gyrus discrepancy in
electronic versions of the Talairach atlas. Neuroimage. 2004 Jan;21(1):450-5.
PUBMED ID: 14741682
The above manuscripts provide a complete description of how the atlas volumes
were generated and validated.

----------------------------------------------------------------------
AAL2 is the implementation of a new parcellation of the orbitofrontal cortex in
the automated anatomical labeling atlas.
Rolls ET, Joliot M & Tzourio-Mazoyer N (2015) . NeuroImage
10.1016/j.neuroimage.2015.07.075
———————
Overview
An alternative parcellation of the orbitofrontal cortex is described for the
automated anatomical labeling atlas of Tzourio-Mazoyer et al. (2002) (Automated
anatomical labeling of activations in SPM using a macroscopic anatomical
parcellation of the MNI MRI single-subject brain. NeuroImage 15:273-289). The
new parcellation of the orbitofrontal cortex follows the description provided
by Chiavaras, Petrides, and colleagues (2000, 2001).

———————
 The AAL atlas is probably the most widely used cortical parcellation map in
 connectomic literature. It can be downloaded from the website:
 http://www.gin.cnrs.fr/AAL2?lang=en and it consists on 120 regions which
 parcellate the cortical and subcortical area.

----------------------------------------------------------------------
AICHA is an atlas of intrinsic connectivity of homotopic areas.
It derives from Joliot M, Jobard G, Naveau M, Delcroix N, Petit L, Zago L,
Crivello F, Mellet E, Mazoyer B & Tzourio-Mazoyer N (2015) . Journal of
Neuroscience Methods 10.1016/j.jneumeth.2015.07.013. (PDF)
 ——————
Overview:
AICHA (for Atlas of Intrinsic Connectivity of Homotopic Areas) is a functional
brain ROIs atlas based on resting-state fMRI data acquired in 281 individuals.
AICHA ROIs cover the whole cerebrum, each having 1- homogeneity of its
constituting voxels intrinsic activity, and 2- a unique homotopic contralateral
counterpart with which it has maximal intrinsic connectivity.  This atlas is
protected by copyright; you can freely use it for none profit research
purposes, providing the above reference is cited. For other use please contact
us through aicha.gin.brainatlas at gmail.com The AICHA atlas includes 192
couples of homotopic regions for a total of 384 regions. AICHA is provided in
the MNI stereotaxic space (MNI ICBM 152, Template sampling size of 2x2x2 mm3
voxels; bounding box, x = -90 to 90 mm, y = -126 to 91 mm, z = -72 to 109 mm).

AICHA atlas includes both regions located in the crown of the gyri (named
Gyrus, region name beginning by “G_”) and regions located in the depth of the
sulci (named Suclus, region name beginning by “S_”). In addition the
subcortical nuclei were labeled separately (name Nucleus, region name beginning
by “N_”).  Different parcels belonging to the same anatomical region were
labeled with numbers (starting to 1). For example the precuneus show as 9
subparts labeled from G_Precuneus-1-L to G_Precuneus-9-L.
——————
Information and download can be found in the website:
http://www.gin.cnrs.fr/AICHA-344?lang=en



----------------------------------------------------------------------
Hammers atlas:

This atlas, based on Alexander Hammers' brain atlas, made available for the
Euripides project, Nov 2009 (A).


If you use these atlases, please cite the references below.


Websites:
A) http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Atlases


References:
1) Hammers A, Allom R, Koepp MJ, Free SL, Myers R, Lemieux L, Mitchell TN,
Brooks DJ, Duncan JS. Three-dimensional maximum probability atlas of the human
brain, with particular reference to the temporal lobe. Hum Brain Mapp 2003, 19:
224-247.
(for the region definitions #01-49 including protocols)

2) Gousias IS, Rueckert D, Heckemann RA, Dyet LE, Boardman JP, Edwards AD,
Hammers A. Automatic segmentation of brain MRIs of 2-year-olds into 83 regions
of interest. Neuroimage 2008 Apr 1;40(2):672-684.
(for region names #50-67 and access to protocols: www.brain-development.org)



--------------------------------------------------------------------------------
LPBA40 atlas:
--------------------------------------------------------------------------------

The LONI Probabilistic Brain Atlas (LPBA40) is a series of maps of brain
anatomic regions. These maps were produced from a set of whole-head MRI of 40
human volunteers. Each MRI was manually delineated to identify a set of 56
structures in the brain, most of which are within the cortex. These
delineations were then transformed into a common atlas space to produce a set
of coregistered anatomical labels. The original MRI data were also transformed
into the atlas space.

Websites:
A) http://www.loni.usc.edu/atlases/Atlas_Detail.php?atlas_id=12
B) http://www.loni.usc.edu/atlases/Atlas_Methods.php?atlas_id=12
C) http://shattuck.bmap.ucla.edu/resources/lpba40/

References:
1) Shattuck DW, Mirza M, Adisetiyo V, Hojatkashani C, Salamon G, Narr KL,
Poldrack RA, Bilder RM, Toga AW (2008) Construction of a 3D Probabilistic Atlas
of Human Cortical Structures, NeuroImage 39 (3): 1064-1070. DOI:
10.1016/j.neuroimage.2007.09.031

This paper should be referenced in any works that use the data provided here.
Any feedback regarding this collection of data can be addressed to David
Shattuck (shattuck@loni.ucla.edu). We encourage investigators who develop
projects based on this collection to let us know about their work.

--------------------------------------------------------------------------------

MICCAI 2012 Grand Challenge and Workshop on Multi-Atlas Labeling:
Neuromorphometrics Atlas
--------------------------------------------------------------------------------

Maximum probability tissue labels derived from the ``MICCAI 2012 Grand
Challenge and Workshop on Multi-Atlas Labeling''
(https://masi.vuse.vanderbilt.edu/workshop2012/index.php/Challenge_Details).
These data were released under the Creative Commons Attribution-NonCommercial
(CC BY-NC) with no end date. Users should credit the MRI scans as originating
from the OASIS project (http://www.oasis-brains.org/) and the labeled data as
"provided by Neuromorphometrics, Inc. (http://Neuromorphometrics.com/) under
academic subscription".  These references should be included in all workshop
and final publications.


Websites:
A) https://masi.vuse.vanderbilt.edu/workshop2012/index.php/Challenge_Details
B) http://www.oasis-brains.org/
C) http://Neuromorphometrics.com/



--------------------------------------------------------------------------------
$Id: neuromorphometrics.txt 817 2015-12-17 14:27:24Z dahnke $
----------------------------------------------------------------------
%############################################################################
% COPYRIGHT:   Copyright 2003 K.J. Worsley
%              Department of Mathematics and Statistics,
%              McConnell Brain Imaging Center,
%              Montreal Neurological Institute,
%              McGill University, Montreal, Quebec, Canada.
%              keith.worsley@mcgill.ca , www.math.mcgill.ca/keith
%
%              Permission to use, copy, modify, and distribute this
%              software and its documentation for any purpose and without
%              fee is hereby granted, provided that this copyright
%              notice appears in all copies. The author and McGill University
%              make no representations about the suitability of this
%              software for any purpose.  It is provided "as is" without
%              express or implied warranty.
%############################################################################
----------------------------------------------------------------------
