Provided by: odin_2.0.5-3build1_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.  This program is part of odin 2.0.5 with
       configuration  using_gcc debug gui(:5) standalone dl  posix_threads  libz  gsl  nifti  vtk
       dicom png ismrmrd gdb

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

       -dce: TE used for field drift calculations, if non-zero [ms] (default=0.0)

       -dcs: Index selection string in recipe used for drift correction (space separated list  of
              'dim=selection', e.g. te=2)

       -dcw: Store field drift to file with this prefix

       -dd: Disable field-drift correction

       -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

       -dt: Disable template-based phase 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
              analyze asc coi dat dcm double float gz h5 hdr idx ima interfile jdx mag mhd

       nii  ph  png  pos  pro  reg  s16bit  s32bit  s8bit  smp u16bit u32bit u8bit vtk xml xpro '
       (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=0.0)

       -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: Scale Factor for the grid used for gridding (default=1.0)

       -gt: Store GRAPPA template images

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

       -j: Number of concurrent jobs(threads) in reco (default=16)

       -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=4.24264)

       -kw2d: Kernel width for 2d k-space gridding [Pixel] (default=3.0)

       -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=3000.0)

       -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), 4(significantDebug), 5(normalDebug), 6(verboseDebug).

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