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voxbo-fileformats(7) [debian man page]

voxbo-fileformats(7)						 The VoxBo Manual					      voxbo-fileformats(7)

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 for-
       mats 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 deriva-
       tives.

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).

VoxBo							      January, 2011 (v1.8.5)					      voxbo-fileformats(7)

Check Out this Related Man Page

NIFTI(1)																  NIFTI(1)

NAME

       nifti - IO libraries and tools for the NIFTI-1 data format

DESCRIPTION

       The  NIfTI-1  data  format  is  a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI
       (fMRI) brain images.

       The NIfTI format is an extension of the widely used ANALYZE 7.5 format. The goals of this modified data format are (1) to  add  information
       to the header that will be useful for functional neuroimaging data analysis and display. These additions include:

	      - More basic data types.
	      - Two affine transformations to specify voxel coordinates.
	      - "Intent" codes and parameters to describe the meaning of the data.
	      - Affine scaling of the stored data values to their "true" values.
	      - Optional storage of the header and image data in one file (.nii).

       And (2) To maintain compatibility with non-NIFTI-aware ANALYZE 7.5 compatible software (i.e., such a program should be able to do something
       useful with a NIFTI-1 dataset -- at least, with one stored in a traditional .img/.hdr file pair).

       The NIfTI library package consists of two libraries:

       znzlib -- low level library for handling read/write of compressed files.

       niftilib -- core i/o routines for reading and writing nifti-1 format files. Primarily routines to  read/write  and  manipulate  the  header
       field information, including orientation matrices.  Volume-wise, timecourse-wise, access to image data.

SEE ALSO

       nifti_tool(1), nifti1_test(1), nifti_stats(1).

       Homepage: http://niftilib.sourceforge.net

AUTHOR

       The NIfTI libraries were written by the NIfTI Data Format Working Group (DFWG, http://nifti.nimh.nih.gov/ ).

       This manual page was written by Michael Hanke <michael.hanke@gmail.com>, for the Debian project (but may be used by others).

Michael Hanke							    August 2006 							  NIFTI(1)
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