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
NoFilter 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
interpolation (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
filling (default=0)
-zr: Minimum size of final image in read direction obtained zero
filling (default=0)
-zs: Minimum size of final image in slice direction obtained zero
filling (default=0)
-v <loglevel> or <component:loglevel> for debugging/tracing all
components 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