table of contents
MIVIEW(1) | User Commands | MIVIEW(1) |
NAME¶
miview - Viewer for medical image filesSYNOPSIS¶
miview [ options ] <image-file>DESCRIPTION¶
miview: Viewer for medical image files- File formats are automatically identified by their file extension.
Global options:¶
-blowup: Enlarge display size by this factor
(default=1)
-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 bitmap(bmp) files and exit, use
the given filename prefix
-legend: Export legend as bitmap to this file
-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).
fMRI options (Give at least -design and -fmri to activate):¶
-bonferr: Use Bonferroni correction
-corr: Error probability threshold for correlation
(default=0.050)
-davg: Smooth the design function using a moving average
filter of width N (TR) (default=0)
-design: Load fMRI design from this file (comma or space
separated)
-fmask: fMRI mask file
-fmri: Load fMRI data from this file
-hrf: Convolve design function by hemodynamic response
function prior to correlation (see Glover NeuroImage 9, 416-429)
-neighb: Minimum next neighbours with significant
activation (default=1)
-scourse: Dump relative fMRI signal change time course to
this file
-smap: Dump map of relative fMRI signal change to this
file
-zmap: Dump z-score map to this file
-zscore: z-Score threshold for correlation
(default=0.0)
File read options:¶
-date: Date of scan [yyyymmdd]
(default=20140807yyyymmdd)
-fp: FOV in phase direction [mm] (default=220.0mm)
-fr: FOV in read direction [mm] (default=220.0mm)
-fs: FOV in slice direction [mm] (default=5.0mm)
-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=00000000yyyymmdd)
-pid: Unique patient identifier (default=Unknown)
-pname: Full patient name (default=Unknown)
-psex: Patients sex (options=M F O , default=O)
-pweight: Patients weight [kg] (default=50.0kg)
-scient: Scientist Name (default=Unknown)
-sd: Inter-slice distance (from center to center) [mm]
(default=10.0mm)
-serd: Series Description (default=Unknown)
-serno: Series Number (default=1)
-st: Slice thickness [mm] (default=5.0mm)
-stud: Study Description (default=Unknown)
-tcname: Name of transmit coil (default=Unknown)
-te: Time-to-echo of the sequence [ms]
(default=80.0ms)
-time: Time of scan [hhmmss] (default=090951hhmmss)
-tr: Time between consecutive excitations [ms]
(default=1000.0ms)
-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
-jdx: If multiple JDX 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 hdr idx ima
interfile jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit
u32bit u8bit , default=autodetect)
-skip: Skip this amount of bytes before reading the raw
data (default=0)
Filters:¶
-align <filename,In-plane blowup factor> : Align
data to the geometry (voxel locations) of an external file
-automask : Create mask using automatic histogram-based
threshold
-cluster : Create clusters of non-zero
adjacent/next-neighbours voxels, sorted by size
-convolve <convolution kernel (Gauss NoFilter Triangle
Hann Hamming CosSq Blackman BlackmanNuttall Exp ),kernel diameter [mm]> :
Convolution in spatial dimensions
-detrend <Number of low frequency components to be
removed,Zero mean of resulting timecourse> : Remove slow drift over
time
-edit <Position/range string in the format
(timeframe,slicepos,phasepos,readpos),new value of voxel> : Edit single
voxel values
-genmask <lower threshold,upper threshold> : Create
mask including all voxels with value in given range
-isotrop <voxelsize [mm]> : make image voxels
isotrop through interpolation (image geometry will not change)
-lowpass <Cut-off frequency [Hz]> : Lowpass
filtering
-max <Maximum value> : 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 <Minumum value> : Clip all values below
mininum value
-minip <direction (time slice phase read none )> :
Perform minimum intensity projection over given direction
-noNaN <Replacement value> : Replaces every NaN by
the given value
-pflip : Flip data in phase direction
-prange <Single value or 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> : Create mask including all
voxels above the given fractional threshold
-resample <new size> : Temporal resize of image
data
-resize <slice-size,phase-size,read-size> : Spatial
resize of image data
-reslice <requested orientation (sagittal coronal
axial )> : reslices the image to a given orientation
-rflip : Flip data in read direction
-rot <angle [deg],kernel size [pixel]> : In-plane
rotation
-rrange <Single value or range, optionally with
increment (e.g. 1-10:3)> : Select range in read direction
-scale <Slope,Offset> : Rescale image values
-sflip : Flip data in slice direction
-shift <readDirection shift [pixel],phaseDirection
shift [pixel],sliceDirection shift [pixel]> : Shift data spatially
-slicetime <space-separated list of slice indices in
order of acquisition> : Correct for different acquisition time points of
slices
-splice <dimension of the data to be spliced (time
slice phase read none )> : splices the image in the given direction
-srange <Single value or range, optionally with
increment (e.g. 1-10:3)> : Select range in slice direction
-swapdim <[rps][-],[rps][-],[rps][-]> :
swap/reflect dimensions by specifying a direction triple with optional
reflection sign appended
-tile <columns> : Combine slices into a square 2D
image
-trange <Single value or range, optionally with
increment (e.g. 1-10:3)> : Select range in time direction
-tshift <time shift [frames]> : Shift data in
time
-typemax <Datatype> : Clip all values above maximum
of a specific datatype
-typemin <Datatype> : Clip all values below mininum
of a specific datatype
-usemask <filename> : Create 1D dataset including
all values within mask from file
Supported file extensions(formats):¶
- 3db
- (Iris3D binary data)
- analyze
- (NIFTI/ANALYZE, dialects: fsl )
- asc
- (ASCII, dialects: tcourse )
- coi
- (JCAMP-DX data sets)
- dat
- (Matlab ascii 2D data matrix)
- dcm
- (DICOM, dialects: siemens )
- double
- (double raw data)
- float
- (float raw data)
- gz
- (GNU-Zip container for other formats)
- hdr
- (Interfile, dialects: neurostat )
- hdr
- (NIFTI/ANALYZE, dialects: fsl )
- idx
- (3D-indices of non-zeroes in ASCII)
- ima
- (DICOM, dialects: siemens )
- interfile
- (Interfile, dialects: neurostat )
- jdx
- (JCAMP-DX image format)
- mag
- (DICOM, dialects: siemens )
- mhd
- (MetaImage)
- nii
- (NIFTI/ANALYZE, dialects: fsl )
- ph
- (DICOM, dialects: siemens )
- png
- (Portable Network Graphics)
- pos
- (x-y positions of non-zeroes in ASCII)
- pro
- (ODIN measurement protocols)
- reg
- (Ansoft HFSS ASCII)
- s16bit
- (signed 16 bit raw data)
- s32bit
- (signed 32 bit raw data)
- s8bit
- (signed 8 bit raw data)
- smp
- (JCAMP-DX data sets)
- u16bit
- (unsigned 16 bit raw data)
- u32bit
- (unsigned 32 bit raw data)
- u8bit
- (unsigned 8 bit raw data)
August 2014 | miview 1.8.8 |