Provided by: odin_1.8.5-2ubuntu1_amd64 bug

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

       -bcw: Correlation weighting of all blades against the mean of all blades (in image space)

       -bf:  Filter  function  for  blade  phase correction (options=Gauss NoFilter Triangle Hann
              Hamming CosSq Blackman BlackmanNuttall Exp , 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)

       -bkf:  Blade-keyhole  filter function (and its arguments) (options=Gauss NoFilter Triangle
              Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=CosSq)

       -bkt:  Blade-keyhole  transition  width   (fraction   of   oversampled   k-space   center)
              (default=0.20)

       -bwf:  Window/Filter  function  for kspace weighting of each blade (options=Gauss NoFilter
              Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=Triangle)

       -bww: Window/Filter width for kspace weighting of each blade (default=1.0)

       -cp: Use direct Fourier transform with conjugate-phase correction instead of gridding

       -dcr: Load field drift from this file

       -dcw: Calculate and store field drift to file with this prefix

       -df: Output format (file extension) of dump files (default=nii)

       -dg: Disable GRAPPA interpolation

       -dh: Disable homodyne reconstruction

       -dm: Disable fieldmap-based multi-frequency reconstruction

       -dp: Prefix of dump files (default=./dump)

       -ds: Disable slice-time correction

       -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 idx ima jdx mag mhd nii  ph  png  pos  pro  reg
              s16bit s32bit s8bit smp u16bit u32bit u8bit vtk ' (default=nii)

       -ff:  k-space  filter  function  (and its arguments) (options=Gauss NoFilter Triangle Hann
              Hamming CosSq Blackman BlackmanNuttall Exp , 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: Scale Factor for the grid used for gridding (default=1.0)

       -ip: Command line args for extra processing of final images (default=none)

       -j: Number of concurrent jobs(threads) in reco (default=4)

       -kg1d: Kernel function for 1d  k-space  gridding  (options=Gauss  NoFilter  Triangle  Hann
              Hamming CosSq Blackman BlackmanNuttall Exp , default=Gauss(0.36169))

       -kg2d:  Kernel  function  for  2d  k-space  gridding (options=Gauss NoFilter Triangle Hann
              Hamming CosSq Blackman BlackmanNuttall Exp , default=Gauss(0.36169))

       -kh: Keyhole reconstruction, e.g. for PROPELLER

       -ks: Store k-space data

       -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)

       -mr:  Maximum  recursion of reconstruction when waiting for blackboard data, zero means no
              recursion (default=100)

       -o: Prefix of output files (default=./image)

       -pc: Combine phase of channels using a phase correction

       -pe: Exponent for magnitude weighting when calculating  combined  phase  of  all  channels
              (default=0.0)

       -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

       -qs: Quality control: Check for spikes in data

       -rd:  Dump  signal  data  and  its  protocol to files with this prefix, do not reconstruct
              images

       -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 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)

       -type:  Image  representation  type  (options=automatic  float double s32bit u32bit s16bit
              u16bit s8bit u8bit , default=automatic)

       -wdialect: Write data using given dialect of the format. (default is no dialect)

       -wp: Store the protocol separately to this file.

       -zp: Minimum size of final image in phase 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).

       -h, --help, -help, --version : Print help text or version information