Provided by: voxbo_1.8.5~svn1246-1ubuntu1_i386
voxbo-fileformats - general information about file format support in
The VoxBo suite of tools for brain image analysis supports a variety of
formats for 1D (vector), 2D (matrix), 3D (volume) and 4D (volume time
File format support in VoxBo is modular - most of the tools can read
and write any supported file format transparently, with output file
formats usually determined by the file extension.
The i/o library supports several special access methods. For 4D files,
filename:mask is used to access the inclusion mask of a 4D file. The
mask is treated as a 3D volume. Similarly, filename:n accesses the nth
volume of the 4D series in filename, where n is an integer and the
first volume is numbered 0.
When writing, VoxBo honors filename tags that can be used to specify
the fileformat or byteorder. Tags are specified in square brackets at
the end of the filename, and multiple tags can be separated within the
brackets by commas. For example, foo[imgdir] can be used to specify
the imgdir file format (useful because imgdir format doesn't have a
standard extension). foo.nii[little] forces little-endian storage for
file formats that allow it.
VoxBo native file formats
VoxBo's native file formats, all supported for read and write, include
.ref (1D), .mat (2D), .cub (3D), and .tes (4D). Although these formats
are not widely supported in external software, they offer some useful
features, including user-editable text headers. gzip-compressed cub
and tes files are supported transparently.
VoxBo supports 3D and 4D NIfTI files (compressed or not) for read and
write. VoxBo does not currently make intelligent use of the
qform/sform orientation information.
VoxBo supports SPM-style Analyze(TM) files, including 3D and 4D files,
as well as 4D time series composed of directories containing 3D files,
for read/write. All individual files are stored in .img/.hdr pairs.
VoxBo supports DICOM (as well as some DICOM-like files in the older
ACR/NEMA format) for reading only. VoxBo supports a corner of the
DICOM standard frequently encountered in brain imaging research,
including mosaic format volumes. Files containing single slice data
are read as 3D volumes. Directories containing multiple files are
generally parsed as 3D or 4D data, as appropriate, as long as no
extraneous files are in the directory.
Text Matrices and Vectors
Plain text files containing just numbers (or comment lines beginning
with #, %, or ;), can be parsed as matrix or vector data.
Pre-built VoxBo binaries are available for Linux, OSX, and Cygwin, and
via the NeuroDebian project (neuro.debian.net) for Debian derivatives.
VoxBo is provided with no warranty whatsoever.
For an historical roster of the VoxBo development team, visit
For detailed help on any VoxBo command-line program, run it with no
arguments. For graphical programs, use the -h flag. For more help
with VoxBo, for information about the mailing list, or to report bugs,
visit the web site at www.voxbo.org.
For general information about VoxBo, see voxbo(7).