.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.2.
.TH MIVIEW "1" "March 2012" "miview 1.8.5" "User Commands"
.SH NAME
miview \- Viewer for medical image files
.SH SYNOPSIS
.B miview
[ \fIoptions \fR] \fI<image-file>\fR
.SH DESCRIPTION
miview: Viewer for medical image files
.IP
File formats are automatically identified by their file extension.
.SS "Global options:"
.HP
\fB\-blowup\fR: Enlarge display size by this factor (default=1)
.HP
\fB\-bright\fR: Relative brightness of display (default=0.0)
.HP
\fB\-color\fR: Use color map to display values
.HP
\fB\-contrast\fR: Relative contrast of display (default=0.0)
.HP
\fB\-dump\fR: Dump all images as bitmap(bmp) files and exit, use the given filename prefix
.HP
\fB\-low\fR: Lower windowing boundary: This value will appear black in display
.HP
\fB\-map\fR: Load overlay map (colored voxels superimposed on image) from this file
.HP
\fB\-maplegend\fR: Export map legend as bitmap to this file
.HP
\fB\-maplow\fR: Lower windowing boundary for overlay map (default=0.0)
.HP
\fB\-maprect\fR: Relative size of rectangles which represent voxels of the overlay map (default=0.60)
.HP
\fB\-mapupp\fR: Upper windowing boundary for overlay map (default=0.0)
.HP
\fB\-noscale\fR: Disable scale in 2D/3D display
.HP
\fB\-rec\fR: Record clicked coordinates and values into this file
.HP
\fB\-upp\fR: Upper windowing boundary: This value will appear white in display
.HP
\fB\-val\fR: Save value of ROI/point selection to this file
.HP
\fB\-v\fR <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).
.SS "fMRI options (Give at least -design and -fmri to activate):"
.HP
\fB\-bonferr\fR: Use Bonferroni correction
.HP
\fB\-corr\fR: Error probability threshold for correlation (default=0.050)
.HP
\fB\-davg\fR: Smooth the design function using a moving average filter of width N (TR) (default=0)
.HP
\fB\-design\fR: Load fMRI design from this file (comma or space separated)
.HP
\fB\-fmask\fR: fMRI mask file
.HP
\fB\-fmri\fR: Load fMRI data from this file
.HP
\fB\-hrf\fR: Convolve design function by hemodynamic response function prior to correlation (see Glover NeuroImage 9, 416\-429)
.HP
\fB\-neighb\fR: Minimum next neighbours with significant activation (default=1)
.HP
\fB\-scourse\fR: Dump relative fMRI signal change time course to this file
.HP
\fB\-smap\fR: Dump map of relative fMRI signal change to this file
.HP
\fB\-zmap\fR: Dump z\-score map to this file
.HP
\fB\-zscore\fR: z\-Score threshold for correlation (default=0.0)
.SS "File read options:"
.HP
\fB\-date\fR: Date of scan [yyyymmdd] (default=20120328yyyymmdd)
.HP
\fB\-fp\fR: FOV in phase direction [mm] (default=220.0mm)
.HP
\fB\-fr\fR: FOV in read direction [mm] (default=220.0mm)
.HP
\fB\-fs\fR: FOV in slice direction [mm] (default=5.0mm)
.HP
\fB\-nr\fR: Number of consecutive measurements (default=1)
.HP
\fB\-nx\fR: Number of points in read direction (default=1)
.HP
\fB\-ny\fR: Number of points in phase direction (default=1)
.HP
\fB\-nz\fR: Number of points in slice direction (default=1)
.HP
\fB\-pbirth\fR: Patients date of birth [yyyymmdd] (default=00000000yyyymmdd)
.HP
\fB\-pid\fR: Unique patient identifier (default=Unknown)
.HP
\fB\-pname\fR: Full patient name (default=Unknown)
.HP
\fB\-psex\fR: Patients sex (options=M F O , default=O)
.HP
\fB\-pweight\fR: Patients weight [kg] (default=50.0kg)
.HP
\fB\-scient\fR: Scientist Name (default=Unknown)
.HP
\fB\-sd\fR: Inter\-slice distance (from center to center) [mm] (default=10.0mm)
.HP
\fB\-serd\fR: Series Description (default=Unknown)
.HP
\fB\-serno\fR: Series Number (default=1)
.HP
\fB\-st\fR: Slice thickness [mm] (default=5.0mm)
.HP
\fB\-stud\fR: Study Description (default=Unknown)
.HP
\fB\-tcname\fR: Name of transmit coil (default=Unknown)
.HP
\fB\-te\fR: Time\-to\-echo of the sequence [ms] (default=80.0ms)
.HP
\fB\-time\fR: Time of scan [hhmmss] (default=165543hhmmss)
.HP
\fB\-tr\fR: Time between consecutive excitations [ms] (default=1000.0ms)
.HP
\fB\-cplx\fR: Treat data as complex and extract the given component (options=none abs pha real imag , default=none)
.HP
\fB\-ds\fR: Dataset index to extract if multiple datasets are read
.HP
\fB\-filter\fR: Read only those datasets which protocol parameter 'key' contains the string 'value' (given in the format 'key=value')
.HP
\fB\-fmap\fR: For reduced memory usage, keep filemapping after reading (raw) data, but writing into the array will result in a crash
.HP
\fB\-jdx\fR: If multiple JDX arrays are present, select this
.HP
\fB\-rdialect\fR: Read data using given dialect of the format. (default is no dialect)
.HP
\fB\-rf\fR: 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)
.HP
\fB\-skip\fR: Skip this amount of bytes before reading the raw data (default=0)
.SS "Filters:"
.HP
\fB\-align\fR <filename,In\-plane blowup factor> : Align data to the geometry (voxel locations) of an external file
.HP
\fB\-automask\fR : Create mask using automatic histogram\-based threshold
.HP
\fB\-detrend\fR <Number of low frequency components to be removed,Zero mean of resulting timecourse> : Remove slow drift over time
.HP
\fB\-genmask\fR <lower threshold,upper threshold> : Create mask including all voxels with value in given range
.HP
\fB\-isotrop\fR <voxelsize> : make image voxels isotrop through interpolation (image geometry will not change)
.HP
\fB\-lowpass\fR <Cut\-off frequency [Hz]> : Lowpass filtering
.HP
\fB\-max\fR <Maximum value> : Clip all values above maximum value
.HP
\fB\-maxip\fR <direction (time slice phase read none )> : Perform maximum intensity projection over given direction
.HP
\fB\-merge\fR : Merge datasets into a single dataset by expanding the time dimension
.HP
\fB\-min\fR <Minumum value> : Clip all values below mininum value
.HP
\fB\-minip\fR <direction (time slice phase read none )> : Perform minimum intensity projection over given direction
.HP
\fB\-noNaN\fR <Replacement value> : Replaces every NaN by the given value
.HP
\fB\-pflip\fR : Flip data in phase direction
.HP
\fB\-prange\fR <Single value or range, optionally with increment (e.g. 1\-10:3)> : Select range in phase direction
.HP
\fB\-proj\fR <direction (time slice phase read none )> : Perform projection over given direction
.HP
\fB\-quantilmask\fR <quantil> : Create mask including all voxels above the given fractional threshold
.HP
\fB\-resample\fR <new size> : Temporal resize of image data
.HP
\fB\-resize\fR <slice\-size,phase\-size,read\-size> : Spatial resize of image data
.HP
\fB\-reslice\fR <requested orientation (sagittal coronal axial )> : reslices the image to a given orientation
.HP
\fB\-rflip\fR : Flip data in read direction
.HP
\fB\-rot\fR <angle [deg],kernel size [pixel]> : In\-plane rotation
.HP
\fB\-rrange\fR <Single value or range, optionally with increment (e.g. 1\-10:3)> : Select range in read direction
.HP
\fB\-scale\fR <Slope,Offset> : Rescale image values
.HP
\fB\-sflip\fR : Flip data in slice direction
.HP
\fB\-shift\fR <readDirection shift [pixel],phaseDirection shift [pixel],sliceDirection shift [pixel]> : Shift data spatially
.HP
\fB\-splice\fR <dimension of the data to be spliced (time slice phase read none )> : splices the image in the given direction
.HP
\fB\-srange\fR <Single value or range, optionally with increment (e.g. 1\-10:3)> : Select range in slice direction
.HP
\fB\-swapdim\fR <[rps][\-],[rps][\-],[rps][\-]> : swap/reflect dimensions by specifying a direction triple with optional reflection sign appended
.HP
\fB\-tile\fR <columns> : Combine slices into a square 2D image
.HP
\fB\-trange\fR <Single value or range, optionally with increment (e.g. 1\-10:3)> : Select range in time direction
.HP
\fB\-typemax\fR <Datatype> : Clip all values above maximum of a specific datatype
.HP
\fB\-typemin\fR <Datatype> : Clip all values below mininum of a specific datatype
.HP
\fB\-usemask\fR <filename> : Create 1D dataset including all values within mask from file
.SS "Supported file extensions(formats):"
.TP
3db
(Iris3D binary data)
.TP
asc
(ASCII, dialects: tcourse )
.TP
coi
(JCAMP\-DX data sets)
.TP
dat
(Matlab ascii 2D data matrix)
.TP
dcm
(DICOM, dialects: siemens )
.TP
double
(double raw data)
.TP
float
(float raw data)
.TP
gz
(GNU\-Zip container for other formats)
.TP
hdr
(NIFTI/ANALYZE, dialects: fsl )
.TP
idx
(3D\-indices of non\-zeroes in ASCII)
.TP
ima
(DICOM, dialects: siemens )
.TP
jdx
(JCAMP\-DX image format)
.TP
mag
(DICOM, dialects: siemens )
.TP
mhd
(MetaImage)
.TP
nii
(NIFTI/ANALYZE, dialects: fsl )
.TP
ph
(DICOM, dialects: siemens )
.TP
png
(Portable Network Graphics)
.TP
pos
(x\-y positions of non\-zeroes in ASCII)
.TP
pro
(ODIN measurement protocols)
.TP
reg
(Ansoft HFSS ASCII)
.TP
s16bit
(signed 16 bit raw data)
.TP
s32bit
(signed 32 bit raw data)
.TP
s8bit
(signed 8 bit raw data)
.TP
smp
(JCAMP\-DX data sets)
.TP
u16bit
(unsigned 16 bit raw data)
.TP
u32bit
(unsigned 32 bit raw data)
.TP
u8bit
(unsigned 8 bit raw data)
.TP
vtk
(Visualization Toolkit)