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Conte69 Human Surface-based Atlas and Reference Data.

Van Essen Lab

22 May 2012


PLEASE READ THIS: SumsDB links WILL NOT WORK: SumsDB suffered a catastrophic failure in 2016 so all of the links on the page will not function. For more information, please view this notice about SumsDB that includes links that may allow one to find the desired data sets.

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


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. 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

6. 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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