ODINRECO(1)

💖 ODINRECO(1) 💖

okay bestie, pull up a chair, because this is odinreco(1) from the User Commands section and she is a lot — but in the best way. ✨

🌸 NAME 🌸

odinreco — automatic reconstruction for ODIN sequences. that's it. that's the whole vibe. she reconstructs. automatically. 🫶

🎀 SYNOPSIS 🎀

odinreco [ options ] -r <input-file-to-be-read>

🦋 DESCRIPTION 🦋

so like. odinreco: automatic reconstruction for ODIN sequences. slay.

odinreco gives you a generic reconstruction for imaging sequences — think spin-warp, EPI, RARE, the whole girl gang — and she is not picky about it either. 🌈 how does she know what to do?? she reads the file recoInfo, which lives on disk right next to your raw data. that file is holding all the lore about the acquired signal, including the k-space position of each acquisition window (ADC). iykyk. 👑

as output, odinreco generates a bunch of files in different image formats — which ones you get depends on the option -f and on which third-party libraries are available to ODIN. and every single one of those filenames starts with the output prefix you gave her. periodt.

this program is part of odin 2.0.5, built with the configuration using_gcc debug gui(:5) standalone dl posix_threads libz gsl nifti vtk dicom png ismrmrd gdb. iconic honestly. 💅

✨ 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 separated list of output formats (file extensions). the 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-space points to discard in auto-calibration lines because of high residuals (default=0.0)
• -gp — number of neighbouring measured k-space lines used for GRAPPA interpolation (default=2)
• -gr — number of neighbours 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=infinite (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

also bestie don't forget the -r <input-file-to-be-read> from the synopsis, she's the one actually holding the raw data you want reconstructed. no -r, no images. 💀

and that's the whole page!! 🎀 this is odinreco 2.0.5, dated October 2021 — go forth and reconstruct, you've got this, no cap. 💜🦋✨