/Caret:Atlases/Conte69 Atlas

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'''Conte69 Atlas'''
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Conte69 Human Surface-based Atlas and Reference Data.
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Van Essen Lab
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22 May 2012
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An improved human surface-based atlas and associated reference data are now availableThe ‘Conte69’ atlas was generated from 69 healthy adults registered to the “164k_fs_LR” surface mesh (Refs 1, 2).
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We are pleased to release the Conte69 human surface-based atlas and associated reference data.  This atlas was generated from 69 healthy adults (“Conte69”) registered to the “fs_LR” surface mesh [1,2].  The current release (version 2) contains additional reference data not included in version 1 (March, 2012 release).
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The atlas dataset includes
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'''The atlas dataset includes'''
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Population-average data derived from the Conte69 subjects:
Population-average data derived from the Conte69 subjects:
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Average midthickness surfaces with good interhemispheric correspondence [1].
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*      Average midthickness surfaces, in register between left and right hemispheres (Ref 1).
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Average cortical myelin maps [2].
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*      Average cortical myelin maps (Ref 2).
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Average T1w and T2w volumes, registered using FSL’s nonlinear FNIRT.
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*      Average cortical thickness, with and without curvature correction.
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*      Average T1w and T2w volumes, registered using FSL’s nonlinear FNIRT.
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Reference data mapped to the Conte69 atlas:
Reference data mapped to the Conte69 atlas:
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• A composite cortical parcellation based on 52 surface-mapped areas [1].
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• The classical Brodmann parcellation [1]
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• Cortical networks reported in resting-state functional connectivity studies [3,4].
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*      A composite cortical parcellation based on 52 surface-mapped areas (Ref 1).
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How do I access the data? The data are freely available in SumsDB (http://sumsdb.wustl.edu/sums/directory.do?id=8291494&dir_name=CONTE69).  Read the next section to decide which archive(s) to download.
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*      The classical Brodmann parcellation (Ref 1)
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*      Cortical networks derived from a resting-state functional connectivity analysis (Ref 3).
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''More to come.'' Standard Freesurfer-processed datasets can be mapped to the fs_LR mesh and viewed on the Conte69 atlas using a ‘freesurfer_to_fs_LR’ script to be released soon (see below).  Also, data from the Human Connectome Project (Refs 4, 5) will be registered to the fs_LR mesh as part of the standard processing pipeline.
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'''How do I access the data?''' The data are available in SumsDB (via
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[http://sumsdb.wustl.edu/sums/directory.do?id=8291494&dir_name=CONTE69]).  Read the next section to decide which particular archives to download.
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'''Choice of surface mesh.''' Two versions of the data are available that differ in the resolution of the surface mesh (Freesurfer vs PALS).
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The '''Conte69_164k_fs_LR''' atlas has higher spatial resolution and is a step closer to the primary Freesurfer data [1].  [‘164k’ is shorthand for 163,842 surface nodes).]
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The '''Conte69_74k_pals''' atlas enables immediate comparison with existing data mapped to the PALS-B12 atlas [6].  [‘74k’ is shorthand for 73,730 surface nodes).]
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'''Conversion''' of existing data from the 164k_fs_LR mesh to the 74k_pals mesh and vice versa can be readily done by a single command-line step (see below).
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*  '''Download and view the Conte69_164k_fs_LR atlas'''. Link to [http://sumsdb.wustl.edu/sums/directory.do?id=8291755&dir_name=Conte69_164k_fs_LR] then click on the ‘disk’ icon for '''atlas_Conte69_164k_fs_LR.zip'''.
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**Unpack the archive.
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** Change to the atlas_Conte69_164k_fs_LR/ directory.
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** Launch caret5 and select the spec file for the left and/or right hemisphere (Conte69_atlas.L.164k_fs_LR.c5.spec, Conte69_atlas.R.164k_fs_LR.c5.spec)
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** Press Load Scenes, then view the various scenes (highlight and double-click).
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** For additional datasets change to the Extra_Conte69_164k_fs_LR/ directory and open one or both ‘long’ spec files that include additional files and scenes (Conte69_atlas.L.long.164k_fs_LR.c5.spec, Conte69_atlas.R.long.164k_fs_LR.c5.spec
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*'''74k_pals mesh'''. Data from the 164k_fs_LR mesh have been registered to the PALS-B12 atlas, which uses a ‘74k_pals’ mesh (shorthand for 73,730 nodes, [6]).  To download this, link to [http://sumsdb.wustl.edu/sums/directory.do?id=8291756&dir_name=Conte69_74k_pals]  then click on the ‘disk’ icon for *atlas_Conte69_74k_pals.zip*
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** Unpack the archive.
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** Change to the atlas_Conte69_74k_fs_LR/ directory.
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** Launch caret5, open the for the left and/or right hemisphere spec file (Conte69_atlas.L.74k_fs_LR.c5.spec, Conte69_atlas.L.74k_fs_LR.c5.spec)
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** Press Load Scenes, then view the various scenes (highlight and double-click).
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Choose a software platform and surface mesh.  The Conte69 atlas is available in versions customized for Caret5 and for Connectome Workbench (“Workbench”) platforms.  The datasets come in three distinct surface meshes.
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164k_fs_LR mesh.  This high-resolution dataset is closest to the original Freesurfer data but has the left and right hemispheres accurately registered to one another using Caret [1].  [‘164k’ is shorthand for 163,842 surface nodes per hemisphere.]
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'''How can I convert (register) additional data between 164k_fs_LR and 74k_pals meshes?'''
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74k_pals mesh. This version enables immediate comparison with existing data mapped to the PALS-B12 atlas [5].  Available only for Caret5.  [‘74k’ is shorthand for 73,730 surface nodes.]
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*      Download and unzip inter-atlas_deformation_maps.zip archive: [http://sumsdb.wustl.edu/sums/directory.do?id=8291757&dir_name=Inter-atlas_deformation_maps]
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32k_fs_LR mesh. This spatially coarser mesh is useful for visualizing ‘dense connectomes’ and other datasets generated by the WU-Minn Human Connectome Project consortium (http://www.humanconnectome.org/).  Available only for Workbench. [‘32k’ is shorthand for 32,492 surface nodes.]
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*      In a terminal window, change (cd) to whichever target directory (fs_L, fs_LR, fs_R, pals_L, pals_R) represents the mesh you desire for the *output* files.
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Download Caret5 atlas datasets
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• 164k_fs_LR mesh. Link to http://sumsdb.wustl.edu/sums/directory.do?id=8293668&dir_name=Conte69_caret5 
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then click on the ‘disk’ icon for Conte69_atlas_v2.LR.164k_fs_LR.c5.zip.
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o Unpack the archive.
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o Change to the Conte69_164k_fs_LR.c5/ directory.
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o Launch caret5 and select the spec file for the left and/or right hemisphere: Conte69_atlas.L.164k_fs_LR.c5.spec, Conte69_atlas.R.164k_fs_LR.c5.spec
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o Press Load Scenes, then view the various scenes (highlight and double-click).
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• 74k_pals mesh. Link to http://sumsdb.wustl.edu/sums/directory.do?id=8291756&dir_name=74k_mesh_caret5 then click on the ‘disk’ icon for atlas_Conte69_74k_pals.zip
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o Unpack the archive.
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o Change to the atlas_Conte69_74k_fs_LR/ directory.
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o Launch caret5, open the left and/or right hemisphere spec file, Conte69_atlas.L.74k_fs_LR.c5.spec, Conte69_atlas.L.74k_fs_LR.c5.spec
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o Press Load Scenes, then view the various scenes (highlight and double-click).
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*      Enter “caret_command –deformation-map-apply”, then follow the displayed command-line instructions in order to register the files of interest.
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Connectome Workbench.  Workbench software will be available for beta-testing in early June, 2012 (See http://www.humanconnectome.org/ for announcement and instructions.)
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Download Workbench atlas datasets. 
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• 164k_fs_LR mesh. Link to http://sumsdb.wustl.edu/sums/directory.do?id=8291758&dir_name=Conte69_workbench). 
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• Click on the ‘disk’ icon for Conte69_atlas-v2.LR.164k_fs_LR.wb.zip
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o Unpack the archive.
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o Change to the Conte69_atlas_164k_wb/ directory.
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o Launch workbench.
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o Open the spec file (Conte69_atlas-v2.LR.164k_fs_LR.wb.spec), and use it as outlined in the Workbench tutorial.
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'''How can I convert (register) standard Freesurfer data to the 164k_fs_LR mesh?''' Data that have been processed by standard Freesurfer ‘recon-all’ (v5.1 or higher) can be converted to the fs_LR mesh using a ‘freesurfer_to_fs_LR’ script and associated dataset available at [http://brainvis.wustl.edu/wiki/index.php/Caret:Download] - Download Freesurfer_to_fs_LR Pipeline Distribution. Instructions are at: [http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs_LR]. This script will let you convert existing or future Freesurfer datasets to the fs_LR format.  This facilitates interhemispheric comparisons in your own data (e.g., symmetries and asymmetries) as well as comparisons with the Conte69 atlas datasets provided herein.
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• 32k_fs_LR mesh. Link to http://sumsdb.wustl.edu/sums/directory.do?id=8293673&dir_name=32k_mesh_workbench. 
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• Click on the ‘disk’ icon for Conte69_atlas-v2.LR.32k_fs_LR.wb.zip
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o Unpack the archive.
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o Change to the 32k_ConteAtlas_v2/ directory.
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o Launch workbench, open the spec file, and use it as outlined in the Workbench tutorial.
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How can I convert (register) additional data between 164k_fs_LR and 74k_pals meshes?
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• Download and unzip inter-atlas_deformation_maps.zip archive: http://sumsdb.wustl.edu/sums/directory.do?id=8291757&dir_name=Inter-atlas_deformation_maps
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• In a terminal window, change (cd) to whichever target directory (fs_L, fs_LR, fs_R, pals_L, pals_R) represents the mesh you desire for the output files.
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• Enter “caret_command –deformation-map-apply”, then follow the displayed command-line instructions in order to register the files of interest.
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'''Additional notes.'''''
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How can I convert (register) standard Freesurfer data to the 164k_fs_LR mesh? See: http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs_LR.  This will let you convert existing or future Freesurfer datasets to the fs_LR formatThis facilitates interhemispheric comparisons in your own data (e.g., symmetries and asymmetries) as well as comparisons with the Conte69 atlas datasets provided herein.  
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Improved atlas surfaces and myelin maps. '' The Conte69 atlas dataset was derived from Freesurfer segmentation, surface reconstruction, and registration to the fsaverage left and right hemispheres, followed by interhemispheric registration to the left-right hybrid atlas, bringing the two hemispheres into geographic correspondence (Ref 1)The current data release benefits from several refinements in surface generation and in the myelin mapping algorithm compared to the published data (Refs 1, 2).
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''Connectome Workbench data format''. The Conte69 atlas dataset is also available in the new Connectome Workbench data format being developed for the Human Connectome Project.  A beta-release of Connectome Workbench will be made available in the summer of 2012.
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Additional notes.
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'''REFERENCES'''.
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Improved atlas surfaces and myelin maps. The Conte69 atlas dataset was derived from Freesurfer segmentation, surface reconstruction, and registration to the fsaverage left and right hemispheres, followed by interhemispheric registration to the left-right hybrid atlas, bringing the two hemispheres into geographic correspondence [1].  The current data release benefits from several refinements in surface generation and in the myelin mapping algorithm compared to the published data [1, 2]. 
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# [http://cercor.oxfordjournals.org/content/early/2011/11/02/cercor.bhr291.full.pdf+html  '''Van Essen et al., (Cerebral Cortex, 2011)''']
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This document is available at http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas
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# [http://cercor.oxfordjournals.org/content/early/2011/11/02/cercor.bhr291.full.pdf+html  '''Glasser and Van Essen (J. Neuroscience, 2011)''']
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#[http://jn.physiology.org/content/106/3/1125.full.pdf+html '''Yeo et al. (J. Neurophysiol., 2011)''']
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(Van Essen, 2005; Glasser and Van Essen, 2011; Power et al., 2011; Yeo et al., 2011; Van Essen, 2011b)
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#[http://www.humanconnectome.org/ '''http://www.humanconnectome.org''']
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#[http://www.sciencedirect.com/science/article/pii/S1053811912001954 '''Van Essen et al., (NeuroImage, 2012)''']
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REFERENCES.
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#[http://brainvis.wustl.edu/resources/-Pals.wcover.pdf '''Van Essen (NeuroImage, 2005)''']
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1. Van Essen DC, Glasser, M.F., Dierker, D., Harwell, J., and Coalson, T. (2011b) Parcellations and hemispheric asymmetries of human cerebral cortex analyzed on surface-based atlases. Cereb Cortex 2 Nov epub ahead of print 10.1093/cercor/bhr291.
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2. Glasser M, Van Essen DC (2011) Mapping human cortical areas in vivo based on myelin content as revealed by T1 and T2-weighted MRI. J Neuroscience 31:11597-11616.
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3. Power JD, Cohen AL, Nelson SM, Wig GS, Barnes KA, Church JA, Vogel AC, Laumann TO, Miezin FM, Schlaggar BL, Petersen SE (2011) Functional network organization of the human brain. Neuron 72:665-678.
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4. Yeo BT, Krienen FM, Sepulcre J, Sabuncu MR, Lashkari D, Hollinshead M, Roffman JL, Smoller JW, Zollei L, Polimeni JR, Fischl B, Liu H, Buckner RL (2011) The organization of the human cerebral cortex estimated by intrinsic functional connectivity. J Neurophysiol 106:1125-1165.
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5. http://www.humanconnectome.org
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6. Van Essen, D.C., Ugurbil, K., Auerbach, E., Barch, D., Behrens, T.E.J., Bucholz, R., Chang, A., Chen, L., Corbetta, M. Curtiss, S. W., Della Penna, S., Feinberg, D., Glasser, M.F., Harel, N., Heath, A.C., Larson-Prior, L., Marcus, D., Michalareas, G., Moeller, S., Oostenveld, R., Petersen,  S.E., Prior, F., Schlaggar, B.L., Smith, S.M., Snyder, A.Z., Xu, J., and Yacoub, E. (2012) The human connectome project: A data acquisition perspective.  Neuroimage. http://dx.doi.org/10.1016/j.neuroimage.2012.02.018
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7. Van Essen DC (2005) A Population-Average, Landmark- and Surface-based (PALS) atlas of human cerebral cortex. NeuroImage 28:635-662.

Revision as of 19:01, 22 May 2012

Conte69 Human Surface-based Atlas and Reference Data. Van Essen Lab 22 May 2012

We are pleased to release the Conte69 human surface-based atlas and associated reference data. This atlas was generated from 69 healthy adults (“Conte69”) registered to the “fs_LR” surface mesh [1,2]. The current release (version 2) contains additional reference data not included in version 1 (March, 2012 release).

The atlas dataset includes Population-average data derived from the Conte69 subjects: • Average midthickness surfaces with good interhemispheric correspondence [1]. • Average cortical myelin maps [2]. • Average T1w and T2w volumes, registered using FSL’s nonlinear FNIRT.

Reference data mapped to the Conte69 atlas: • A composite cortical parcellation based on 52 surface-mapped areas [1]. • The classical Brodmann parcellation [1] • Cortical networks reported in resting-state functional connectivity studies [3,4].

How do I access the data? The data are freely available in SumsDB (http://sumsdb.wustl.edu/sums/directory.do?id=8291494&dir_name=CONTE69). Read the next section to decide which archive(s) to download.

Choose a software platform and surface mesh. The Conte69 atlas is available in versions customized for Caret5 and for Connectome Workbench (“Workbench”) platforms. The datasets come in three distinct surface meshes.

164k_fs_LR mesh. This high-resolution dataset is closest to the original Freesurfer data but has the left and right hemispheres accurately registered to one another using Caret [1]. [‘164k’ is shorthand for 163,842 surface nodes per hemisphere.]

74k_pals mesh. This version enables immediate comparison with existing data mapped to the PALS-B12 atlas [5]. Available only for Caret5. [‘74k’ is shorthand for 73,730 surface nodes.]

32k_fs_LR mesh. This spatially coarser mesh is useful for visualizing ‘dense connectomes’ and other datasets generated by the WU-Minn Human Connectome Project consortium (http://www.humanconnectome.org/). Available only for Workbench. [‘32k’ is shorthand for 32,492 surface nodes.]

Download Caret5 atlas datasets • 164k_fs_LR mesh. Link to http://sumsdb.wustl.edu/sums/directory.do?id=8293668&dir_name=Conte69_caret5 then click on the ‘disk’ icon for Conte69_atlas_v2.LR.164k_fs_LR.c5.zip. o Unpack the archive. o Change to the Conte69_164k_fs_LR.c5/ directory. o Launch caret5 and select the spec file for the left and/or right hemisphere: Conte69_atlas.L.164k_fs_LR.c5.spec, Conte69_atlas.R.164k_fs_LR.c5.spec o Press Load Scenes, then view the various scenes (highlight and double-click).

• 74k_pals mesh. Link to http://sumsdb.wustl.edu/sums/directory.do?id=8291756&dir_name=74k_mesh_caret5 then click on the ‘disk’ icon for atlas_Conte69_74k_pals.zip o Unpack the archive. o Change to the atlas_Conte69_74k_fs_LR/ directory. o Launch caret5, open the left and/or right hemisphere spec file, Conte69_atlas.L.74k_fs_LR.c5.spec, Conte69_atlas.L.74k_fs_LR.c5.spec o Press Load Scenes, then view the various scenes (highlight and double-click).

Connectome Workbench. Workbench software will be available for beta-testing in early June, 2012 (See http://www.humanconnectome.org/ for announcement and instructions.)

Download Workbench atlas datasets. • 164k_fs_LR mesh. Link to http://sumsdb.wustl.edu/sums/directory.do?id=8291758&dir_name=Conte69_workbench). • Click on the ‘disk’ icon for Conte69_atlas-v2.LR.164k_fs_LR.wb.zip o Unpack the archive. o Change to the Conte69_atlas_164k_wb/ directory. o Launch workbench. o Open the spec file (Conte69_atlas-v2.LR.164k_fs_LR.wb.spec), and use it as outlined in the Workbench tutorial.

• 32k_fs_LR mesh. Link to http://sumsdb.wustl.edu/sums/directory.do?id=8293673&dir_name=32k_mesh_workbench. • Click on the ‘disk’ icon for Conte69_atlas-v2.LR.32k_fs_LR.wb.zip o Unpack the archive. o Change to the 32k_ConteAtlas_v2/ directory. o Launch workbench, open the spec file, and use it as outlined in the Workbench tutorial.

How can I convert (register) additional data between 164k_fs_LR and 74k_pals meshes? • Download and unzip inter-atlas_deformation_maps.zip archive: http://sumsdb.wustl.edu/sums/directory.do?id=8291757&dir_name=Inter-atlas_deformation_maps • In a terminal window, change (cd) to whichever target directory (fs_L, fs_LR, fs_R, pals_L, pals_R) represents the mesh you desire for the output files. • Enter “caret_command –deformation-map-apply”, then follow the displayed command-line instructions in order to register the files of interest.

How can I convert (register) standard Freesurfer data to the 164k_fs_LR mesh? See: http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs_LR. This will let you convert existing or future Freesurfer datasets to the fs_LR format. This facilitates interhemispheric comparisons in your own data (e.g., symmetries and asymmetries) as well as comparisons with the Conte69 atlas datasets provided herein.

Additional notes.

Improved atlas surfaces and myelin maps. The Conte69 atlas dataset was derived from Freesurfer segmentation, surface reconstruction, and registration to the fsaverage left and right hemispheres, followed by interhemispheric registration to the left-right hybrid atlas, bringing the two hemispheres into geographic correspondence [1]. The current data release benefits from several refinements in surface generation and in the myelin mapping algorithm compared to the published data [1, 2].

This document is available at http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas

(Van Essen, 2005; Glasser and Van Essen, 2011; Power et al., 2011; Yeo et al., 2011; Van Essen, 2011b)

REFERENCES.

1. Van Essen DC, Glasser, M.F., Dierker, D., Harwell, J., and Coalson, T. (2011b) Parcellations and hemispheric asymmetries of human cerebral cortex analyzed on surface-based atlases. Cereb Cortex 2 Nov epub ahead of print 10.1093/cercor/bhr291. 2. Glasser M, Van Essen DC (2011) Mapping human cortical areas in vivo based on myelin content as revealed by T1 and T2-weighted MRI. J Neuroscience 31:11597-11616. 3. Power JD, Cohen AL, Nelson SM, Wig GS, Barnes KA, Church JA, Vogel AC, Laumann TO, Miezin FM, Schlaggar BL, Petersen SE (2011) Functional network organization of the human brain. Neuron 72:665-678. 4. Yeo BT, Krienen FM, Sepulcre J, Sabuncu MR, Lashkari D, Hollinshead M, Roffman JL, Smoller JW, Zollei L, Polimeni JR, Fischl B, Liu H, Buckner RL (2011) The organization of the human cerebral cortex estimated by intrinsic functional connectivity. J Neurophysiol 106:1125-1165. 5. http://www.humanconnectome.org 6. Van Essen, D.C., Ugurbil, K., Auerbach, E., Barch, D., Behrens, T.E.J., Bucholz, R., Chang, A., Chen, L., Corbetta, M. Curtiss, S. W., Della Penna, S., Feinberg, D., Glasser, M.F., Harel, N., Heath, A.C., Larson-Prior, L., Marcus, D., Michalareas, G., Moeller, S., Oostenveld, R., Petersen, S.E., Prior, F., Schlaggar, B.L., Smith, S.M., Snyder, A.Z., Xu, J., and Yacoub, E. (2012) The human connectome project: A data acquisition perspective. Neuroimage. http://dx.doi.org/10.1016/j.neuroimage.2012.02.018 7. Van Essen DC (2005) A Population-Average, Landmark- and Surface-based (PALS) atlas of human cerebral cortex. NeuroImage 28:635-662.

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