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
-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=20120328yyyymmdd)
-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=165543hhmmss)
-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 asc coi
dat dcm double float gz hdr idx ima jdx mag mhd nii ph png pos pro reg s16bit
s32bit s8bit smp u16bit u32bit u8bit vtk , 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
-detrend
<Number of low frequency components to be removed,Zero mean of resulting
timecourse> : Remove slow drift over time
-genmask
<lower threshold,upper threshold> : Create mask including all voxels
with value in given range
-isotrop
<voxelsize> : 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 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
-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
-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)
- 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
- (NIFTI/ANALYZE, dialects: fsl )
- idx
- (3D-indices of non-zeroes in ASCII)
- ima
- (DICOM, dialects: siemens )
- 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)
- vtk
- (Visualization Toolkit)
March 2012 | miview 1.8.5 |