ODINRECO(1)
NAME
odinreco - Automatic reconstruction for ODIN sequences
SYNOPSIS
odinreco [ options ] -r <input-file-to-be-read>
DESCRIPTION
odinreco: Automatic reconstruction for ODIN sequences
odinreco provides a generic reconstruction for imaging
sequences (spin-warp, EPI, RARE, ...). It retrieves the information about the acquired signal from the file 'recoInfo' which is
stored on disk together with the raw data. The recoInfo file
contains information about the k-space position of each acquisition
windows (ADC). As output, odinreco generates a bunch of files with
different image formats (depending on the option -f and third-party
libraries available to ODIN). The filename of each file starts with the
given output prefix.
OPTIONS
- -bf: Filter function for blade phase correction (options=Gauss NoFilter
- Triangle Hann Hamming CosSq Blackman BlackmanNuttall , default=NoFilter)
- -bfw: Width of the filter function used for blade phase correction.[0.0
- (0%) ... 1.0 (100%) of blade width; -1.0 (100%) ... 0.0 (0%) of center width] (default=1.0)
- -cp: Use direct Fourier transform with conjugate-phase correction
- instead of gridding
- -df: Output format (file extension) of dump files (default=nii)
- -dh: Disable homodyne reconstruction
- -dm: Disable fieldmap-based multi-frequency reconstruction
- -dp: Prefix of dump files (default=./dump)
- -dr: Dump signal data and its protocol to files with this prefix, do
- not reconstruct images
- -el: Level relative to mean value of first echo for setting mask of
- exponential decay fit (default=0.50)
- -f: Space sepapared list of output formats (file extensions), possible
- formats are '3db asc coi dat dcm double float gz hdr ima jdx mag mhd nii ph png pos reg s16bit s32bit s8bit smp u16bit u32bit u8bit v vtk ' (default=nii)
- -ff: k-space filter function (and its arguments) (options=Gauss NoFil
- ter Triangle Hann Hamming CosSq Blackman BlackmanNuttall , default=NoFilter)
- -fm: Load fieldmap data from this file
- -fp: Filter plateau width (0=no plateau, 1=full plateau) (default=0.0)
- -gd: Fraction of k-psace points to discard in auto-calibration lines
- because of high residuals (default=0.010)
- -gp: Number of neigbouring measured k-space lines used for GRAPPA
- interpolation (default=2)
- -gr: Number of neigbours in read direction used for GRAPPA interpola
- tion (default=5)
- -gs: Truncation value of SVD (i.e. regularization) when calculating
- GRAPPA weights (default=1.00000e-03)
- -ip: Command line args for extra processing of final images
- (default=none)
- -j: Number of concurrent jobs(threads) in reco (default=4)
- -kf: Blade-keyhole filter function (and its arguments) (options=Gauss
- NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall , default=CosSq)
- -kg1d: Kernel function for 1d k-space gridding (options=Gauss NoFilter
- Triangle Hann Hamming CosSq Blackman BlackmanNuttall , default=Gauss(0.36169))
- -kg2d: Kernel function for 2d k-space gridding (options=Gauss NoFilter
- Triangle Hann Hamming CosSq Blackman BlackmanNuttall , default=Gauss(0.36169))
- -ks: Store k-space data
- -kt: Blade-keyhole transition width (fraction of oversampled k-space
- center) (default=0.20)
- -kw1d: Kernel width for 1d k-space gridding [Pixel]
- (default=4.24264Pixel)
- -kw2d: Kernel width for 2d k-space gridding [Pixel] (default=3.0Pixel)
- -mf: Maximum number of frequencies for multi-frequency reconstruction
- (default=256)
- -mn: In sliding-window maximum-intensity projection, use this number of
- neighbors in each direction (default=4)
- -o: Prefix of output files (default=./image)
- -pc: Combine phase of channels using a phase correction
- -pf: File name of FIFO (named pipe) to obtain the raw data from
- -pop: Recipe for post processing of 3D volume after channel combining
- (default=null)
- -prp: Recipe for post processing of 3D volume before channel combining
- (default=null)
- -pt: Combine and store phase timecourse from all channels
- -pz: Pad missing raw data (of interrupted measurement) with zeroes
- -rf: Read reco recipe (pipeline layout) from this file
- -rp: Reco recipe (pipeline layout)
- -s: Select certain dimensions ranges (space separated list of
- 'dim=selection', e.g. slice=3)
- -sc: Store images from channels separately instead of combining them
- -sp: Store phase in addition to magnitude
- -sw: Sliding window, and if possible keyhole, reconstruction, e.g. for
- Spiral/PROPELLER
- -t1f: Use this type of T1 fit, can be one of 'simple', 'magnitude'
- (default=simple)
- -t1l: Level relative to mean value of first echo for setting mask of T1
- fit (default=0.50)
- -t1m: Upper limit for T1 fit [ms] (default=3000.0ms)
- -to: Timeout for reco in seconds, 0=inifinite (default=0)
- -wdialect: Write data using given dialect of the format. (default is no
- dialect)
- -zp: Minimum size of final image in read direction obtained zero fill
- ing (default=0)
- -zr: Minimum size of final image in read direction obtained zero fill
- ing (default=0)
- -zs: Minimum size of final image in slice direction obtained zero fill
- ing (default=0)
- -v <loglevel> or <component:loglevel> for debugging/tracing all compo
- nents or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog), 4(significantDebug), 5(normalDebug), 6(verboseDebug).
- -h, --help, -help, --version : Print help text or version information