Cobra atlas:
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CAT12 was used to segment the T1 data and to estimate the registration parameters to transform the probability maps to MNI152NLin2009cAsym space. 

The resulting maximum probability map was slightly modified: (1) remaining holes were filled with median value, (2) an additionally mask with brainmask_T1.nii was applied to remove non-brain areas.
Furthermore, the different labels were merged and re-labeled with unique IDs.

The Cobra atlas is build from 5 atlases that are provided by the Computational Brain Anatomy Laboratory at the Douglas Institute (CoBra Lab). The 5 atlases are based on high-resolution (0.3mm isotropic voxel size) images of the amygdala, hippocampus, subcortical structures and the cerebellum. Please note that the original labels were changed in order to allow a combined atlas.

High-resolution in vivo atlases of the hippocampal subfields
============================================================

This atlas is described in: 

    Winterburn JL, Pruessner JC, Chavez S, Schira MM, Lobaugh NJ, Voineskos AN,
    Chakravarty MM. A novel in vivo atlas of human hippocampal subfields using high-
    resolution 3 T magnetic resonance imaging. Neuroimage. 2013 Jul 1;74:254-65.

Please cite this paper when using the atlas. 

High-resolution in vivo atlases of the amygdala
=================================================

These atlases are described in: 

     Treadway MT, Waskom ML, Dillon DG, et al. Illness Progression, Recent
     Stress, and Morphometry of Hippocampal Subfields and Medial Prefrontal Cortex
     in Major Depression. Biol Psychiatry. 2014;

Please cite this paper when using these atlases. 

These atlases are defined on the same subjects as the Cerebellar and
Hippocampal subfield atlases. 

The manual segmentation protocol used to produce these atlases is described in: 

    Entis JJ, Doerga P, Barrett LF, Dickerson BC. A reliable protocol for the
    manual segmentation of the human amygdala and its subregions using ultra-high
    resolution MRI. Neuroimage. 2012;60(2):1226-35.

Labels 
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Label: 26  - left amygdala
Label: 126 - right amygdala

Extra-Hippocampal White Matter Atlas + Hippocampal Subfields
=====================================================================

These images, atlases, the corresponding manual segmentation protocol, as well as 
their validation for use in the MAGeT Brain automatic segmentation pipeline are 
fully described in:

    Amaral, R.S.C., Park, M.T.M., Devenyi, G.A., Pruessner, J.C., Pipitone, J., 
    Winterburn, J., Chavez, S., Schira, M., Lobaugh, N., Voineskos, A.N., 
    Chakravarty, M.M, and Alzheimer's Disease Neuroimaging Initiative (2016). 
    Manual segmentation of the fornix, fimbria, and alveus on high-resolution 
    3T MRI: Application via fully-automated mapping of the human memory circuit 
    white and grey matter in healthy and pathological aging. NeuroImage. 
    (doi:10.1016/j.neuroimage.2016.10.027)

To obtain the subject T1 and T2 images for these labels, or for more
information, please visit: 

http://cobralab.ca/atlases/Hippocampus-whitematter/
http://cobralab.ca/atlases/Hippocampus-subfields/


Labels 
------

Label: 31  - left CA1
Label: 32  - left subiculum
Label: 33  - left fornix
Label: 34  - left CA4/dentate gyrus
Label: 35  - left CA2/CA3
Label: 36  - left stratum radiatum/stratum lacunosum/stratum moleculare
Label: 37  - left fimbria
Label: 38  - left mammillary body
Label: 39  - left alveus
Label: 131 - right CA1
Label: 132 - right subiculum
Label: 133 - right fornix
Label: 134 - right CA4/dentate gyrus
Label: 135 - right CA2/CA3
Label: 136 - right stratum radiatum/stratum lacunosum/stratum moleculare
Label: 137 - right fimbria
Label: 138 - right mammillary body
Label: 139 - right alveus

High-resolution in vivo atlases of the cerebellum
=================================================


These atlases, and the manual segmentation protocol used to produce them are described in: 

    Park, M.T., Pipitone, J., Baer, L., Winterburn, J.L., Shah, Y., Chavez, S.,
    Schira, M.M., Lobaugh, N.J., Lerch, J.P., Voineskos, A.N., Chakravarty, M.M.
    Derivation of high-resolution MRI atlases of the human cerebellum at 3T and segmentation 
    using multiple automatically generated templates. Neuroimage. 2014; 95: 217-31.

To obtain the subject T1 and T2 images for these labels, or for more
information, please visit: 

  http://cobralab.ca/atlases/Cerebellum/

Labels 
------

Label: 11   - left I-II
Label: 12   - left III
Label: 13   - left IV
Label: 14   - left V
Label: 15   - left VI
Label: 16   - left Crus I
Label: 17   - left Crus II
Label: 18   - left VIIB
Label: 19   - left VIIIA
Label: 20  - left VIIIB
Label: 21  - left IX
Label: 22  - left X
Label: 23  - left CM
Label: 111 - right I-II
Label: 112 - right III
Label: 113 - right IV
Label: 114 - right V
Label: 115 - right VI
Label: 116 - right Crus I
Label: 117 - right Crus II
Label: 118 - right VIIB
Label: 119 - right VIIIA
Label: 120 - right VIIIB
Label: 121 - right IX
Label: 122 - right X
Label: 123 - right CM

Subcortical Atlases of the striatum, globus pallidus and thalamus
===================================================================

When using these atlases, please cite:

    Tullo,S., Devenyi, G.A., Patel, R., Park, M.T.M., Collins, D.L. & 
    Chakravarty, M.M. (In submission). Warping an atlas derived from 
    serial histology to 5 high-resolution MRIs. Scientific Data.

Labels
------
	1   - left striatum 
	2   - left globus pallidus 
	3   - left thalamus 
	101 - right striatum 
	102 - right globus pallidus 
	103 - right thalamus

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