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.
Usage: odinreco [ options ] -r <input-file-to-be-read>
Options:
-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
-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)
-hf: Dump Siemens header to this file
-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
