table of contents
ODINRECO(1) | User Commands | ODINRECO(1) |
NAME¶
odinreco - Automatic reconstruction for ODIN sequencesSYNOPSIS¶
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
-dce: TE used for field drift calculations, if non-zero
[ms] (default=0.0ms)
-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
-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
hdr idx ima interfile jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit
smp u16bit u32bit u8bit ' (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=24)
-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
August 2014 | odinreco 1.8.8 |