xenial (7) voxbo-fileformats.7.gz

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).