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MIVIEW

MIVIEW

Section: User Commands (1) Updated: January 2010
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NAME

miview - Viewer for medical image files  

SYNOPSIS

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), 4(significantDebug), 5(normalDebug), 6(verboseDebug).
 

fMRI options (Give at least -design and -fmri to activate):

-bonferr: Use Bonferroni correction
-corr: Error probability for correlation (default=1.00000e-03)
-design: Load fMRI design from this file (comma or space separated)
-fmask: fMRI mask file
-fmri: Load fMRI data from this file
-neighb: Minimum next neighbours with significant activation (default=1)
 

File read options:

-date: Date of scan [yyyymmdd] (default=20100109yyyymmdd)
-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=121904hhmmss)
-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 ima jdx mag mhd nii ph png pos reg s16bit s32bit s8bit smp u16bit u32bit u8bit v 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
-detrend <Number of low frequency components to be removed> : 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)
-max <Maximum value> : Clip all values above maximum value
-merge : Merge datasets into a single dataset by expanding the time dimension
-min <Minumum value> : Clip all values below mininum value
-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
-resize <slice-size,phase-size,read-size> : Resize 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 dimension
-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 using mask from file
 

Supported file extensions(formats):

3db
(Iris3D binary data)
asc
(ASCII)
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 )
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)
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)
v
(Vista, dialects: common odin lipsia )
vtk
(Visualization Toolkit)


 

Index

NAME
SYNOPSIS
DESCRIPTION
Global options:
fMRI options (Give at least -design and -fmri to activate):
File read options:
Filters:
Supported file extensions(formats):

This document was created by man2html, using the manual pages.
Time: 21:23:55 GMT, April 16, 2011