ODINRECO(1)							   User Commands						       ODINRECO(1)

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  BlackmanNut-
	      tall 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

odinreco 1.8.5							    March 2012							       ODINRECO(1)