PARREC2NII(1) User Commands PARREC2NII(1)NAME
parrec2nii - convert PARREC image to NIfTI
SYNOPSIS
parrec2nii [OPTIONS] <PAR files>
DESCRIPTION
PAR/REC to NIfTI converter
OPTIONS --version
show program's version number and exit
-h, --help
show this help message and exit
-v, --verbose
Make some noise.
-o OUTDIR, --output-dir=OUTDIR
Destination directory for NIfTI files. Default: current directory.
-c, --compressed
Whether to write compressed NIfTI files or not.
--origin=ORIGIN
Reference point of the q-form transformation of the NIfTI image. If 'scanner' the (0,0,0) coordinates will refer to the scanner's
iso center. If 'fov', this coordinate will be the center of the recorded volume (field of view). Default: 'scanner'.
--minmax=MINMAX
Mininum and maximum settings to be stored in the NIfTI header. If any of them is set to 'parse', the scaled data is scanned for the
actual minimum and maximum. To bypass this potentially slow and memory intensive step (the data has to be scaled and fully loaded
into memory), fixed values can be provided as spaceseparated pair, e.g. '5.4 120.4'. It is possible to set a fixed minimum as scan
for the actual maximum (and vice versa). Default: 'parse parse'.
--store-header
If set, all information from the PAR header is stored in an extension of the NIfTI file header. Default: off
--scaling=SCALING
Choose data scaling setting. The PAR header defines two different data scaling settings: 'dv' (values displayed on console) and 'fp'
(floating point values). Either one can be chosen, or scaling can be disabled completely ('off'). Note that neither method will
actually scale the data, but just store the corresponding settings in the NIfTI header. Default: 'dv'
parrec2nii 1.2.2 June 2012 PARREC2NII(1)
Check Out this Related 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)