odinreco(1)
Automatic reconstruction for ODIN sequences
Description
ODINRECO
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
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-bcw: Correlation weighting of all blades against the mean of all blades (in image space) | |
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-bf: Filter function for blade phase correction (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=NoFilter) | |
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-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) | |
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-bkf: Blade-keyhole filter function (and its arguments) (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=CosSq) | |
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-bkt: Blade-keyhole transition width (fraction of oversampled k-space center) (default=0.20) | |
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-bwf: Window/Filter function for kspace weighting of each blade (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=Triangle) | |
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-bww: Window/Filter width for kspace weighting of each blade (default=1.0) | |
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-cp: Use direct Fourier transform with conjugate-phase correction instead of gridding | |
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-dce: TE used for field drift calculations, if non-zero [ms] (default=0.0) | |
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-dcs: Index selection string in recipe used for drift correction (space separated list of ’dim=selection’, e.g. te=2) | |
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-dcw: Store field drift to file with this prefix | |
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-dd: Disable field-drift correction | |
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-df: Output format (file extension) of dump files (default=nii) | |
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-dg: Disable GRAPPA interpolation | |
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-dh: Disable homodyne reconstruction | |
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-dm: Disable fieldmap-based multi-frequency reconstruction | |
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-dp: Prefix of dump files (default=./dump) | |
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-ds: Disable slice-time correction | |
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-dt: Disable template-based phase correction | |
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-el: Level relative to mean value of first echo for setting mask of exponential decay fit (default=0.50) | |
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-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)
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-ff: k-space filter function (and its arguments) (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=NoFilter) | |
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-fm: Load fieldmap data from this file | |
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-fp: Filter plateau width (0=no plateau, 1=full plateau) (default=0.0) | |
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-gd: Fraction of k-psace points to discard in auto-calibration lines because of high residuals (default=0.0) | |
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-gp: Number of neigbouring measured k-space lines used for GRAPPA interpolation (default=2) | |
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-gr: Number of neigbours in read direction used for GRAPPA interpolation (default=5) | |
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-gs: Scale Factor for the grid used for gridding (default=1.0) | |
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-gt: Store GRAPPA template images | |
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-ip: Command line args for extra processing of final images (default=none) | |
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-j: Number of concurrent jobs(threads) in reco (default=16) | |
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-kg1d: Kernel function for 1d k-space gridding (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=Gauss(0.36169)) | |
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-kg2d: Kernel function for 2d k-space gridding (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=Gauss(0.36169)) | |
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-kh: Keyhole reconstruction, e.g. for PROPELLER | |
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-ks: Store k-space data | |
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-kw1d: Kernel width for 1d k-space gridding [Pixel] (default=4.24264) | |
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-kw2d: Kernel width for 2d k-space gridding [Pixel] (default=3.0) | |
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-mf: Maximum number of frequencies for multi-frequency reconstruction (default=256) | |
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-mn: In sliding-window maximum-intensity projection, use this number of neighbors in each direction (default=4) | |
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-mr: Maximum recursion of reconstruction when waiting for blackboard data, zero means no recursion (default=100) | |
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-o: Prefix of output files (default=./image) | |
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-pc: Combine phase of channels using a phase correction | |
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-pe: Exponent for magnitude weighting when calculating combined phase of all channels (default=0.0) | |
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-pf: File name of FIFO (named pipe) to obtain the raw data from | |
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-pop: Recipe for post processing of 3D volume after channel combining (default=null) | |
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-prp: Recipe for post processing of 3D volume before channel combining (default=null) | |
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-pt: Combine and store phase timecourse from all channels | |
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-pz: Pad missing raw data (of interrupted measurement) with zeroes | |
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-qs: Quality control: Check for spikes in data | |
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-rd: Dump signal data and its protocol to files with this prefix, do not reconstruct images | |
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-rf: Read reco recipe (pipeline layout) from this file | |
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-rp: Reco recipe (pipeline layout) | |
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-s: Select certain dimensions ranges (space separated list of ’dim=selection’, e.g. slice=3) | |
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-sc: Store images from channels separately instead of combining them | |
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-sp: Store phase in addition to magnitude | |
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-sw: Sliding window reconstruction, e.g. for Spiral/PROPELLER | |
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-t1f: Use this type of T1 fit, can be one of ’simple’, ’magnitude’ (default=simple) | |
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-t1l: Level relative to mean value of first echo for setting mask of T1 fit (default=0.50) | |
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-t1m: Upper limit for T1 fit [ms] (default=3000.0) | |
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-to: Timeout for reco in seconds, 0=inifinite (default=0) | |
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-type: Image representation type (options=automatic float double s32bit u32bit s16bit u16bit s8bit u8bit , default=automatic) | |
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-wdialect: Write data using given dialect of the format (default is no dialect) | |
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-wp: Store the protocol separately to this file. | |
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-zp: Minimum size of final image in phase direction obtained zero filling (default=0) | |
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-zr: Minimum size of final image in read direction obtained zero filling (default=0) | |
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-zs: Minimum size of final image in slice direction obtained zero filling (default=0) | |
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-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). | |
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-h, --help, -help, --version : Print help text or version information |