This is the command miview that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
-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)
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