Caret6:FileFormats

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File Formats

Caret5 was able to read and write a large number of data file formats. In Caret6, the supported file formats have been greatly consolidated compared to Caret5. Whenever possible, neuroimaging standard file formats (GIFTI and NIFTI) are used. By using the neuroimaging standard file formats, it allows the users to move their data between neuroimaging software applications without having to perform any file format conversions. For data that does not fit within the standard neuroimaging file formats, Caret6 specific XML files are used.

For volume data, only the NIFTI file format is supported.

Caret5 had some Caret format data files that were written in ASCII and/or binary format. Even in Caret5, these formats presented problems in regards to Unicode (internationalized character sets) and mixing of ASCII and binary data. These files have been replaced with XML files to alleviate these problems.

Please note that most file Caret5 file formats cannot be read by Caret6. Likewise, most Caret6 file formats cannot be read by Caret5. A conversion program is available that converts Caret5 file formats into Caret6 file formats. However, there is no conversion of Caret6 file formats into Caret5 file formats.

Surfaces Replace Coordinates and Topology

In Caret5, surface files were not used. Instead, the coordinates and topology (triangles) were stored in separate files. While this provided great flexibility, it also presented a couple of problems. Most importantly, all other neuroimaging software applications used surface files which presented problems with exchanging data files. Secondly, there was the occasional problem involving a missing topology file. As a result, Caret6 is designed for surface files instead of the separate coordinate and topology files.

Color Files Are Eliminated

In Caret5, several different color files were available for border files, foci files, paint files, and paint volumes. In Caret6, these separate color files are no longer needed. Instead, the colors are stored within the border, foci, label (paint), and label volume files.

Supported Formats

  • Caret XML Files contain Caret6 unique data.
  • GAR (GIFTI Archive) is a Java JAR (Java Archive) file that contains multiple data file of the same type such as metric or volumes.
  • GIFTI XML is the standard neuroimaging file format for surface-based data.
  • NIFTI is the standard neuroimaging file format for volume-based data.

Converting Files from Caret5 to Caret6 Formats

To convert data files from Caret5 to Caret6 formats, the program caret_command, included in the Caret5 distribution, may be used.

  • Use "caret_command -caret6-convert-spec-file" to convert a Caret5 Specification File and its data files into Caret6 format files.
  • Use "caret_command -caret6-convert-data-file" to convert individual Caret5 data files into Caret6 format file.

Note that these commands write the new files into the current directory. It is best to run the command from a new, empty directory and convert files that are located elsewhere.

Caret6 Files

File Format XML Schema Extension Description
Border Projection Caret XML Download .borderproj Borders are lines drawn on surfaces to identify areas or for registration landmarks.
Color GIFTI Download *color Color files should not be needed in Caret6.
Coordinate GIFTI Download .coord.gii Coordinatefiles should not be used in Caret6.
Foci Projection Caret XML Download .fociproj Foci are 3D symbols drawn at 3D locations of neuroimaging activations.
Foci Search Caret XML Download .focisearch Allow searches of foci on foci attributes.
GIFTI Archive Java JAR N/A *.gar A Java JAR file containing GIFTI files of one type.
Image GIF, JPG, PNG N/A .gif .jpg .png Standard image file formats.
Label GIFTI Download .label.gii Labels assigned to surface nodes providing identification information such as Brodmann areas.
Metric (Functional) GIFTI Download .func.gii A measurement at each node, often used for functional imaging data.
Shape GIFTI Download .shape.gii A shape measurement, such as curvature, at each node.
Specification Caret XML Download .spec Organizes a set of related data files such as those for a single subject.
Study Metadata Caret XML Download .study Information about studies (journal articles). Typically linked from other data.
Surface GIFTI Download .surf.gii A 3D surface, typically of the cerebral cortex.
Topology GIFTI Download .topo.gii Topology files should not be used in Caret6.
Vector GIFTI Download .vector.gii Vectors at 3D locations.
Vocabulary Caret XML Download .vocabulary Vocabulary of neuroimaging names.
Volume NIFTI N/A .nii, .nii.gz Volumetric data such as MRI or fMRI.


Schemas Referenced by the Data File Schemas:

GAR (Gifti Archive Files

NOTE: Perhaps this should be a CAR file (Caret Archive File) since it is likely that non-GIFTI files will be incorporated.

A GAR file is Java JAR file that contains data files readable by Caret6. A Java JAR files is really a ZIP file to which special files are added (MANIFEST.MF).

When creating a JAR file, create the JAR file WITHOUT using compression. This allows for fast access to files within the JAR file. To create a JAR file, run the command "jar cf0 <jar-file-name.jar> <filenames>". The options CF0 (C, F, Zero) mean Create a File with no (0) compression.

Reference: The Java Archive (JAR) File Format

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