File formats
are automatically identified by their file extension.
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
|
-blowup: Enlarge display
size by this factor (0=automatic) (default=0) |
|
-bright: Relative
brightness of display (default=0.0) |
|
-color: Use color map to
display values |
|
-contrast: Relative
contrast of display (default=0.0) |
|
-dump: Dump all images as
graphic files and exit, use the given filename postfix to
specify the format |
|
-legend: Export legend to
this file, use the given filename postfix to specify the
format |
|
-low: Lower windowing
boundary: This value will appear black in display |
|
-map: Load overlay map
(colored voxels superimposed on image) from this file |
|
-maplegend: Export map
legend as bitmap to this file |
|
-maplow: Lower windowing
boundary for overlay map (default=0.0) |
|
-maprect: Relative size
of rectangles which represent voxels of the overlay map
(default=0.60) |
|
-mapupp: Upper windowing
boundary for overlay map (default=0.0) |
|
-noscale: Disable scale
in 2D/3D display |
|
-rec: Record clicked
coordinates and values into this file |
|
-upp: Upper windowing
boundary: This value will appear white in display |
|
-val: Save value of
ROI/point selection to this file |
|
-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). |
File read options:
|
-aa: azimuthal rotation angle [deg]
(default=0.0) |
|
-ah: height rotation angle [deg]
(default=0.0) |
|
-ai: inplane rotation angle [deg]
(default=0.0) |
|
-date: Date of scan [yyyymmdd]
(default=20211015) |
|
-fp: FOV in phase direction [mm]
(default=220.0) |
|
-fr: FOV in read direction [mm]
(default=220.0) |
|
-fs: FOV in slice direction [mm]
(default=5.0) |
|
-nr: Number of consecutive measurements
(default=1) |
|
-nx: Number of points in read direction
(default=1) |
|
-ny: Number of points in phase direction
(default=1) |
|
-nz: Number of points in slice direction
(default=1) |
|
-pbirth: Patients date of birth [yyyymmdd]
(default=00000000) |
|
-pid: Unique patient identifier
(default=Unknown) |
|
-pname: Full patient name (default=Unknown) |
|
-psex: Patients sex (options=M F O ,
default=O) |
|
-psize: Patients size/height [mm]
(default=2000.0) |
|
-pweight: Patients weight [kg] (default=50.0) |
|
-rcname: Name of receive coil
(default=Unknown) |
|
-scient: Scientist Name (default=Unknown) |
|
-sd: Inter-slice distance (from center to center)
[mm] (default=10.0) |
|
-serd: Series Description (default=Unknown) |
|
-serno: Series Number (default=1) |
|
-st: Slice thickness [mm] (default=5.0) |
|
-stud: Study Description (default=Unknown) |
|
-tcname: Name of transmit coil
(default=Unknown) |
|
-te: Time-to-echo of the sequence [ms]
(default=80.0) |
|
-time: Time of scan [hhmmss] (default=104558) |
|
-tr: Time between consecutive excitations [ms]
(default=1000.0) |
|
-cplx: Treat data as complex and extract the
given component (options=none abs pha real imag ,
default=none) |
|
-ds: Dataset index to extract if multiple
datasets are read |
|
-filter: Read only those datasets which protocol
parameter ’key’ contains the string
’value’ (given in the format
’key=value’) |
|
-fmap: For reduced memory usage, keep filemapping
after reading (raw) data, but writing into the array will
result in a crash |
|
-framesplit: Force splitting frames with
different acquisition times into separate protocol-data
pairs |
|
-ldr: If multiple LDR (labeled data record)
arrays are present, select this |
|
-rdialect: Read data using given dialect of the
format (default is no dialect) |
|
-rf: Read format, use it to override file
extension (options=autodetect 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=autodetect) |
|
-skip: Skip this amount of bytes before reading
the raw data (default=0) |
Filters:
|
-align <filename,In-plane blowup factor
(default=0)> : Align data to the geometry (voxel
locations) of an external file |
|
-automask <skip leftmost slots
(default=0),dump histogram,dump histogram fit> : Create
binary mask using automatic histogram-based threshold |
|
-cluster : Create clusters of non-zero
adjacent/next-neighbours voxels, sorted by size |
|
-convolve <convolution kernel
(default=noFunction) (Gauss NoFilter Triangle Hann Hamming
CosSq Blackman BlackmanNuttall Exp
),full-width-at-half-maximum of kernel [mm]
(default=0.0)> : Convolution in spatial dimensions |
|
-detrend <Number of low frequency components
to be removed (default=5),Zero mean of resulting timecourse
(default=No)> : Remove slow drift over time |
|
-dilate <radius of kernel [mm]
(default=0.0)> : dilate image using spherical kernel as
structuring element |
|
-edit <string in the format
(timerange,slicerange,phaserange,readrange),value
(default=0.0)> : Edit voxel values with range specified
as single position, or ’all’, or explicit range,
optionally with increment (e.g. 1-10:3) |
|
-erode <radius of kernel [mm]
(default=0.0)> : erode image using spherical kernel as
structuring element |
|
-genmask <lower threshold (default=0.0),upper
threshold (default=0.0)> : Create binary mask including
all voxels with value in given range |
|
-inv : Invert image values, i.e. lowest to
highest and vice versa |
|
-isotrop <voxelsize [mm] (default=0.0)> :
make image voxels isotrop through interpolation (image
geometry will not change), set to zero for minimum
extent |
|
-lowpass <Cut-off frequency [Hz]
(default=0.0)> : Lowpass filtering |
|
-max <Maximum value (default=0.0)> : Clip
all values above maximum value |
|
-maxip <direction (time slice phase read none
)> : Perform maximum intensity projection over given
direction |
|
-merge : Merge datasets into a single dataset by
expanding the time dimension |
|
-min <Minimum value (default=0.0)> : Clip
all values below minimum value |
|
-minip <direction (time slice phase read none
)> : Perform minimum intensity projection over given
direction |
|
-noNaN <Replacement value (default=0.0)> :
Replaces every NaN by the given value |
|
-nonzeromask : Create binary mask including all
voxels with non-zero value |
|
-pflip : Flip data in phase direction |
|
-prange <single position, or
’all’, or explicit range, optionally with
increment (e.g. 1-10:3)> : Select range in phase
direction |
|
-proj <direction (time slice phase read none
)> : Perform mean projection over given direction |
|
-quantilmask <quantil (default=0.0)> :
Create binary mask including all voxels above the given
fractional threshold |
|
-resample <new size (default=0)> : Temporal
resize of image data |
|
-resize <slice-size (default=0),phase-size
(default=0),read-size (default=0)> : Spatial resize of
image data |
|
-reslice <requested orientation
(default=coronal) (sagittal coronal axial )> : reslices
the image to a given orientation |
|
-rflip : Flip data in read direction |
|
-rot <angle [deg] (default=0.0),kernel size
[pixel] (default=1.41421)> : In-plane rotation |
|
-rrange <single position, or
’all’, or explicit range, optionally with
increment (e.g. 1-10:3)> : Select range in read
direction |
|
-scale <Slope (default=1.0),Offset
(default=0.0)> : Rescale image values |
|
-sflip : Flip data in slice direction |
|
-shift <readDirection shift [pixel]
(default=0.0),phaseDirection shift [pixel]
(default=0.0),sliceDirection shift [pixel] (default=0.0)>
: Shift data spatially |
|
-slicetime <space-separated list of slice
indices in order of acquisition> : Correct for different
acquisition time points of slices |
|
-spheremask <Position string in the format
(slicepos,phasepos,readpos),radius [mm] (default=0.0)> :
Create binary spherical mask |
|
-splice <dimension of the data to be spliced
(time slice phase read none )> : splices the image in the
given direction |
|
-srange <single position, or
’all’, or explicit range, optionally with
increment (e.g. 1-10:3)> : Select range in slice
direction |
|
-sum <direction (time slice phase read none
)> : Perform sum projection over given direction |
|
-swapdim <[rps][-],[rps][-],[rps][-]> :
swap/reflect/transpose dimensions by specifying a direction
triple with optional reflection sign appended |
|
-tile <columns (default=0)> : Combine
slices into a square 2D image |
|
-trange <single position, or
’all’, or explicit range, optionally with
increment (e.g. 1-10:3)> : Select range in time
direction |
|
-tshift <time shift [frames] (default=0.0)>
: Shift data in time |
|
-typemax <Datatype> : Clip all values above
maximum of a specific datatype |
|
-typemin <Datatype> : Clip all values below
minimum of a specific datatype |
|
-usemask <filename> : Create 1D dataset
including all values within binary mask from file |