CARET and Surface-Based Atlases

Caret (Computerized Anatomical Reconstruction and Editing Toolkit) is designed for interactively viewing, manipulating, and analyzing surface reconstructions of the cerebral and cerebellar cortex.
 

Preview Caret and its atlases in slide shows and movies

Slides

HTML slide show of Human Atlas

Microsoft PowerPoint slide show of Human Atlas

HTML slide show of Macaque Atlas

Microsoft PowerPoint slide show of Macaque Atlas

Movies

MPEG Movie of a spin around the human right hemisphere

MPEG Movie scrolling through the human atlas structural MRI

MPEG Movie scrolling through the human atlas segmented cerebral and cerebellar cortex

MPEG Movie of a spin around the macaque right hemisphere

MPEG Movie scrolling through the macaque atlas structural MRI

MPEG Movie scrolling through the macaque atlas segmented cerebral and cerebellar cortex

Slides and Movies Package

Tutorials and Documentation for Caret 5.51

Caret 5.551 Advanced Quick Start Tutorial PDF Dataset

Caret 5.504 Quick Start Tutorial PDF Dataset

Caret 5.5 Tutorial - The Basics (including PALS atlas)

Caret 5.5 Tutorial - User's Guide to Analysis Procedures

Caret 5.5 Tutorial - Segmentation, Flattening, and Registration

Caret 5.5 Tutorial - Contours and Sections

Caret GUI Reference Guide

Caret 5.51 List of Changes

Tutorials and Documentation for Caret 5.4

Caret 5.402 Menu Reference Guide

Caret 5.402 List of Changes

Tutorials and Documentation for Caret 5.33

The PALS Human Cortical Atlas Tutorial Using Caret5 Software (v. 5.3) 16 June 2005

Caret5 Spherical Registration Core 6 Landmark Set

Caret 5.33 Menu Reference Guide

Caret 5.33 List of Changes

Tutorials and Documentation for Caret 5.2

Caret 5.2 Tutorial - Introduction, Installation, Visualization, and Registration (PDF)

Caret 5.2 Tutorial - Population-Average Landmark- and Surface-based Atlas (PDF)

Caret 5.2 Tutorial - Segmentation and Flattening (PDF)

Caret 5.2 Menu Reference Guide

Tutorials and Documentation for Caret 5.1

Caret 5.1 Quick Start Guide (PDF)

Data Set for use with Caret 5.1 Quick Start Guide (.tar.gz archive for UNIX users)

Data Set for use with Caret 5.1 Quick Start Guide (.zip archive for Windows users)

Caret 5.1 User's Manual and Tutorial (PDF)

Data Set for use with Caret 5.1 User's Manual and Tutorial (.tar.gz archive for UNIX users)

Data Set for use with Caret 5.1 User's Manual and Tutorial (.zip archive for Windows Users)

Tutorials and documentation for Caret 4.6

Caret 5 Quick Start (PDF)

Caret 4.6 Quick Start (PDF)

Caret-AFNI Quick Start (PDF)

Caret User's Guide and Tutorial Part 1 (PDF) For use with Tutorial data sets 1 to 4.

Caret User's Guide and Tutorial Part 2 (PDF) For use with Tutorial data sets 5 to 11.

Caret On-Line Reference Manual (HTML, for version 4.40)

Caret Reference Manual (PDF)

Download Tutorial Data Sets for Caret 4.6

Some of the tutorials are available in both gzipped tar files and zip files. Tutorial data sets 1 to 4 are described in Part I of the Caret User's Guide and Tutorial. Tutorial data sets 5 to 11 are described in Part II of the Caret User's Guide and Tutorial. NOTE: The atlas data sets contained in the tutorials are not as up-to-date as those used in Download or View Atlas Data Sets.

Quick Start Tutorial - Caret: gzip-tar   zip

Quick Start Tutorial - Caret-AFNI: gzip-tar   zip

Tutorial 1 HUMAN.COLIN.ATLAS: gzip-tar   zip

Tutorial 2 MACAQUE.F99UA1.ATLAS: gzip-tar   zip

Tutorial 3 REGISTER_HUMAN_MACAQUE: gzip-tar   zip

Tutorial 4 RODENT.ATLASES: gzip-tar   zip

Tutorial 5 FLATTEN.Occipital: gzip-tar

Tutorial 6 FLATTEN.FullHem: gzip-tar

Tutorial 7 REGISTER_SPHERE: gzip-tar

Tutorial 8 REGISTER_FLAT: gzip-tar

Tutorial 9 RECONSTRUCT_SECTIONS: gzip-tar

Tutorial 10 REGISTER_SECTIONS_to_MACAQUE: gzip-tar

Tutorial 11 Part 1 - FREESURFER-to-CARET_DEMO: gzip-tar

Tutorial 11 Part 2 - START-UP_FILES_FREESURFER-to-CARET.MACAQUE: gzip-tar

Jörn Diedrichsen's Caret Surface Statistics

Jörn Diedrichsen, Johns Hopkins University Department of Biomedical Engineering, has developed a SPM-like toolkit for carrying out Caret Surface Statistics. While the Van Essen Lab has not tested/validated these tools, we think many Caret users will find them quite useful. The toolkit includes a brief paper outlining the principles and testing.

Publications

Register for Caret

Download Caret Programs and Source Code

This step requires the ID and password you received when you registered for Caret. 

Go to the download programs and source code page.

Download or View Atlas Data Sets.

About Caret

• Surface visualization
• Display many types of experimental data:
• cortical geography (sulci, gyri, lobes);
• cortical areas (defined anatomically and/or functionally);
• neuroimaging data (fMRI or PET activation patterns);
• connectivity patterns (labeled neurons);
• topographic organization of visual areas;
• surface-based coordinates.
• View data in flexible combinations:
• surface node coloration, representing multiple characteristics
• contours outlining identified regions;
• probabilistic maps derived from many individuals;
• text display of characteristics of highlighted nodes.
• Display surfaces in many configurations:
• fiducial, inflated, spherical, and flat maps;
• rapid toggling between any two concurrently loaded configurations;
• pan, zoom, rotate, and select standard views.
• Surface manipulation and data analysis
• generate inflated maps, spherical maps, and flat maps;
• deform flat maps and spherical maps to an atlas, based on geographic and/or functional landmarks;
• edit surface geometry (align sections, apply cuts, etc.);
• project 3-D data (labeled neurons, activation foci) onto surface;
• draw boundaries (closed or open contours);
• assign node characteristics to contour-enclosed regions.
• Convenient file manipulation
• Natural file groupings organized into "surface specification files";
• Key file attributes are accessible for preview/review via file headers
• Importing and exporting to multiple surface geometry formats (VTK, BYU)

WebCaret is surface visualization software that allows online visualization of dta sets in the Sums DB website. It has many of the visualization capabilities of Caret.

Getting Help / Mailing List

• subscribe by web -- caret-users info page; or
• subscribe by email -- caret-users-join@pulvinar.wustl.edu

You can unsubscribe from caret-users at any time:

• unsubscribe by web -- caret-users info page; or
• unsubscribe by email -- caret-users-leave@pulvinar.wustl.edu

Citing Atlases & Software

When Caret, SureFit, surface-based atlases, or SumsDB datasets from the Van Essen lab are used for scientific publications and presentations (seminars, posters), it is important to provide appropriate acknowledgment. In general, we ask that citations include relevant publication(s) and web site(s):

Caret and SureFit:

Van Essen, D.C., Dickson, J., Harwell, J., Hanlon, D., Anderson, C.H. and Drury, H.A. 2001. An Integrated Software System for Surface-based Analyses of Cerebral Cortex. Journal of American Medical Informatics Association, 8(5): 443-459.

Caret website: http://brainmap.wustl.edu/caret

Surface-based atlas(es):

Human PALS-B12 atlas:

Van Essen, D.C. (2005) A population-average, landmark- and surface-based (PALS) atlas of human cerebral cortex. Neuroimage 28: 635-662

Human Colin cerebellar atlas:

Van Essen, D.C. (2002) Windows on the brain. The emerging role of atlases and databases in neuroscience. Curr. Op. Neurobiol. 12: 574-579

Macaque F99 cerebral and cerebellar atlas:

Van Essen, D.C. (2002) Windows on the brain. The emerging role of atlases and databases in neuroscience. Curr. Op. Neurobiol. 12: 574-579

The following review is a useful additional citation when discussing both the PALS-B12 and macaque F99 atlases:

Van Essen, D.C. and Dierker, D. (2007) Surface-based and probabilistic atlases of primate cerebral cortex.  Neuron 56:209-225.

The SumsDB database

SumsDB website: http://sumsdb.wustl.edu/sums

If you are referencing a specific dataset or archive (e.g., data from your published study uploaded to SumsDB, it can be identified as a specific archive or by the directory in which the archive resides.

Example archive (PALS-B12 standard dataset):
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6571220

OR (with the archive name appended): http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6571220&archive_name=PALS_B12.BOTH-HEMS.STANDARD-SCENES.73730.spec

Example directory:
http://sumsdb.wustl.edu/sums/directory.do?id=636032

OR (with directory name appended): 
http://sumsdb.wustl.edu/sums/directory.do?id=636032&dir_name=ATLAS_DATA_SETS

Publications describing SumsDB:

Van Essen, D.C., Harwell, J., Hanlon, D, and Dickson, J. (2005) Surface-Based Atlases and a Database of Cortical Structure and Function. In: Databasing the Brain: From Data to Knowledge (Neuroinformatics). S.H. Koslow and S. Subramaniam, eds., John Wiley & Sons, NJ, pp. 369-387

Dickson, J., Drury, H., and Van Essen, D.C. (2001) The surface management system (SuMS) database: A surface-based database to aid cortical surface reconstruction, visualization and analysis. Phil. Trans. Royal Soc, Ser B 356:1277-1292