/Caret:Atlases/Conte69 Atlas

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  • Conte69 Atlas*

An improved human surface-based atlas and associated reference data are now available.  The ‘Conte69’ atlas was generated from 69 healthy adults registered to the “164k_fs_LR” surface mesh [1,2].

  • _The atlas dataset includes_*

Population-average data derived from the Conte69 subjects:

·       Average midthickness surfaces, in register between left and right hemispheres [1].

·       Average cortical myelin maps [2].

·       Average cortical thickness, with and without curvature correction.

·       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 derived from a resting-state functional connectivity analysis [3].

_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 [4, 5] will be registered to the fs_LR mesh as part of the standard processing pipeline.

  • _How do I access the data?_**  *The data are available in SumsDB (via

[1]).  Read the next section to decide which particular archives to download.

  • _Choice of surface mesh.  _*Two versions of the data are available that differ in the resolution of the surface mesh (Freesurfer vs PALS).

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)_.]

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)_.]

  • _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).

·       *_Download and view the Conte69_164k_fs_LR atlas_*. Link to [2] then click on the ‘disk’ icon for *atlas_Conte69_164k_fs_LR.zip.*

o   Unpack the archive.

o   Change to the atlas_Conte69_164k_fs_LR/ directory.

o   Launch caret5 and select the spec file for the left and/or right hemisphere:      Human_Conte69_atlas.L.164k_fs_LR.c5.spec, Human_Conte69_atlas.R.164k_fs_LR.c5.spec

o   Press Load Scenes, then view the various scenes (highlight and double-click).

o   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.

Human_Conte69_atlas.L.long.164k_fs_LR.c5.spec, Human_Conte69_atlas.R.long.164k_fs_LR.c5.spec

·       *_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 [3]  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 for the left and/or right hemisphere spec file, Human_Conte69_atlas.L.74k_fs_LR.c5.spec, Human_Conte69_atlas.L.74k_fs_LR.c5.spec

o   Press Load Scenes, then view the various scenes (highlight and double-click).

  • _How can I convert (register) additional data between 164k_fs_LR and 74k_pals meshes? _*

·       Download and unzip inter-atlas_deformation_maps.zip archive: [4]

·       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?   _*Data that have been processed by standard Freesurfer ‘recon-all’ (v5.1 only? Or 5.0 and 5.1?) can be converted to the fs_LR mesh using a ‘freesurfer_to_fs_LR’ script and associated dataset available at [5] - Download Freesurfer_to_fs_LR Pipeline Distribution. Instructions are at: [6].  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.
  • _ _*
  • _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].

_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.

  • REFERENCES*.

1.     Van Essen et al., (Cerebral Cortex, 2011)

2.     Glasser and Van Essen (J. Neuroscience, 2011)

3.     Yeo et al. (J. Neurophysiol., 2011)

4.     [7]

5.     Van Essen et al., (NeuroImage, 2012)

6.     Van Essen (NeuroImage, 2005)

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