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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).

   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)