Caret6:SurfaceBasedAtlases

From Van Essen Lab

Jump to: navigation, search

Contents

Surface-Based Atlases

Naming of JAR File

JAR files containing surface-based atlases must begin with the text "SurfaceAtlas" and end with the ".jar" extension.

Location of JAR File

The JAR files containing the surface-based atlases must be located in the user's class path.

For Caret development in NetBeans, the JAR files are set as a JAR file required by the main class by right-clicking the project, selecting properties from the menu, selecting Libraries in the Categories list, pressing Add JAR/Folder button and selecting the JAR file. When the project is built, the JAR file is copied along with the other dependent JAR files.

Contents of JAR File

Surface-based Atlases are stored in a JAR file in Caret6. The directory structure within the JAR file organizes the data files by stereotaxic space and structure.

  • name-of-atlas
    • stereotaxic-space
      • structure-name
        • data-file-directory which is one of AVERAGE, INDIVIDUALS, or TOPOLOGY.

AVERAGE contains the average coordinate file, INDIVIDUALS contains the individual subject coordinate files, and TOPOLOGY contains the TOPOLOGY file that is used with the coordinate files in both the AVERAGE and INDIVIDUALS directories. If the atlas contains just a single subject, its coordinate file should be in the AVERAGE directory. For multi-subject atlases, the coordinate file in the AVERAGE directory is the average of the individual coordinate files in the INDIVIDUALS directory.

List below are the data files from the PALS atlas in 711-C stereotaxic space. Note that the Cerebellum contains just a single subject and the CortexLeft and CortexRight structures contains both individual files and an average coordinate file.

PALS/711-2C/Cerebellum/AVERAGE/Human.colin.cerebellum.LR.FIDUCIAL.711-2C.Resampled.align.73730.coord
PALS/711-2C/Cerebellum/TOPOLOGY/Human.sphere_6.RIGHT_HEM.73730.topo
PALS/711-2C/CortexLeft/AVERAGE/Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_711-2C.clean.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case01.L.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case02.L.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case03.L.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case04.L.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case05.L.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.clean.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case06.L.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.clean.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case07.L.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case08.L.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case09.L.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case10.L.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case11.L.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexLeft/INDIVIDUALS/Human_Buck_Case12.L.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexLeft/TOPOLOGY/Human.sphere_6.LEFT_HEM.73730.topo
PALS/711-2C/CortexRight/AVERAGE/Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_711-2C.clean.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case01.R.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case02.R.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case03.R.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case04.R.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.clean.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case05.R.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case06.R.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.clean.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case07.R.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case08.R.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case09.R.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case10.R.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case11.R.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexRight/INDIVIDUALS/Human_Buck_Case12.R.M.RegToPALS_B12.LR.FIDUCIAL_711-2C.align.73730.coord
PALS/711-2C/CortexRight/TOPOLOGY/Human.sphere_6.RIGHT_HEM.73730.topo
Personal tools
Sums Database