Brain Innovation

Developer Guide (2.6) - The Format of STC Files

A STC file (STC = "slice time course") contains the functional data (time series) of a FMR project. A FMR project links to the STC file with an "STC Prefix". If the name of the FMR project is, for example, "CG_OBJECTS.fmr", the STC prefix will be "CG_OBJECTS" after project creation. In older releases of BrainVoyager, STC files were not stored in a single file, but in a set of files, each containing the content (repeated measures) of one functional slice. The "StorageDataFormat" entry in the FMR file describes which of four possible arrangements of the STC data are used in a given project. Note that the content in the file(s) are not changed when different storage formats are used, the only thing what changes is the arrangement of the data within one (default) or more (old approach) files.

The STC prefix changes automatically when the data is preprocessed reflecting any applied preprocessing steps but it can also be changed manually to any name, if desired. When BrainVoyager accesses time course data, it uses the STC prefix and a slice number to access the correct information from a STC file.

Single-Slice Format

The single-slice format is the default format in BrainVoyager QX. The order of the data within the single slice is specified by the value of the "StorageDataFormat" in the corresponding FMR file. While there are 3 different arrangements of the data within a single STC file (values 2, 3, and 4), FMR-STC projects only use storage format "2" (for formats "3" and "4", see DWI files). Storage format "2" specifies that the all data of the first slice is stored before the data of the second slice and so on (this is similar as in the old multi-slice format, but the data from different slices is contained in a single file). The data of a single STC file simply contains as many images as there are repeated measurements of the slice. This number is referred to as "NrOfVolumes" within the FMR text file. Each image is assumed to have the dimensions specified as "ResolutionX" and "ResolutionY" in the corresponding FMR file. Note that the STC file does not contain any header information.

Each data element (intensity value) is represented either in 2 bytes (unsigned short) or in 4 bytes (float, default) as determined by the "DataFormat" entry in the FMR file. The data is organized in four loops (most inner loop on the right):

Slices > TimePoints > Rows > Columns - Data

Since the two inner loops address all pixels of an image, we can express this storage arrangement also as:

Slices > TimePoints > ImagePixels - Data

Multi-slice format (deprecated)

This format was used in older versions of BrainVoyager and is also compatible with the most recent versions. The value "1" in the "StorageDataFormat" entry in a FMR file assumes that the data is stored in multiple STC files as in old versions. If the STC prefix is "CG_OBJECTS-" and the number of slices is "15", then it assumes that 15 STC files exist in the same folder as the FMR project with the names:

CG_OBJECTS-1.stc
CG_OBJECTS-2.stc
:
CG_OBJECTS-15.stc

A single STC file simply contains as many images as there are repeated measurements of the slice. This number is referred to as "NrOfVolumes" within the FMR text file. Prior to the series of images, a very short header is defined, containing only the image dimensions "NrOfRows" and "NrOfColumns" as 2 byte values (unsigned short). These two values are compared with the "ResolutionY" and "ResolutionX" values of the corresponding FMR project.

Within each file, each data element (intensity value) is represented in 2 bytes (unsigned short). The data is organized in three loops (most inner loop on the right):

TimePoints > Rows > Columns - Data

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