odinreco: Automatic reconstruction for ODIN sequences
The program 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 -r <input-file-to-be-read>
optional arguments:
-cp: Use direct Fourier transform with conjugate-phase correction instead of gridding
-dr: Dump signal data and its protocol to files with this prefix, do not reconstruct images
-f: Space sepapared list of output formats (file extensions), possible formats are 'asc coi dat dcm double float gz hdr ima img jdx mag mhd nii ph pos s16bit s32bit s8bit smp u16bit u32bit u8bit v vtk ' (default=v)
-ff: Filter function (and its arguments) (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall , default=NoFilter)
-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 magnitude (default=0.0)
-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 used for GRAPPA interpolation when using separate GRAPPA template (default=0.020)
-j: Number of concurrent jobs(threads) in reco (default=8)
-kg: Kernel function for k-space gridding (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall , default=Gauss(0.36169))
-kw: Kernel width for 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)
-pp: Recipe for post processing of 3D volume (default=null)
-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
-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)
-t2l: Level relative to mean value of first echo for setting mask of T2 fit (default=0.50)
-t2m: Upper limit for T2 fit [ms] (default=2000.0ms)
-to: Timeout for reco in seconds, 0=inifinite (default=0)
-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 sinlge component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog), 4(significantDebug), 5(normalDebug), 6(verboseDebug).
