NAME

       voxbo-fileformats - general information about file format support in VoxBo

DESCRIPTION

       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 series) data.

       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.

   NIfTI
       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.

   Analyze
       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.

   DICOM
       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.

EXAMPLES

AVAILABILITY

       Pre-built VoxBo binaries are available for Linux, OSX, and Cygwin, and via the NeuroDebian
       project (neuro.debian.net) for Debian derivatives.

CAVEATS

       VoxBo is provided with no warranty whatsoever.

AUTHOR

       For an historical roster of the VoxBo development team, visit www.voxbo.org.

SEE ALSO

       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).