.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.1.
.TH MIVIEW "1" "October 2021" "miview 2.0.5" "User Commands"
.SH NAME
miview \- Viewer for medical image files
.SH SYNOPSIS
.B miview
[ \fI\,options \/\fR] \fI\,<image-file>\/\fR
.SH DESCRIPTION
miview: Viewer for medical image files
.IP
File formats are automatically identified by their file extension.
.PP
This program is part of odin 2.0.5 with configuration  using_gcc debug gui(:5) standalone dl posix_threads libz gsl nifti vtk dicom png ismrmrd gdb
.SS "Global options:"
.HP
\fB\-blowup\fR: Enlarge display size by this factor (0=automatic) (default=0)
.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 graphic files and exit, use the given filename postfix to specify the format
.HP
\fB\-legend\fR: Export legend to this file, use the given filename postfix to specify the format
.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), 4(significantDebug), 5(normalDebug), 6(verboseDebug).
.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 "ROIs options (Use -rois to activate):"
.HP
\fB\-rois\fR: Activate ROIs mode
.SS "File read options:"
.HP
\fB\-aa\fR: azimuthal rotation angle [deg] (default=0.0)
.HP
\fB\-ah\fR: height rotation angle [deg] (default=0.0)
.HP
\fB\-ai\fR: inplane rotation angle [deg] (default=0.0)
.HP
\fB\-date\fR: Date of scan [yyyymmdd] (default=20211015)
.HP
\fB\-fp\fR: FOV in phase direction [mm] (default=220.0)
.HP
\fB\-fr\fR: FOV in read direction [mm] (default=220.0)
.HP
\fB\-fs\fR: FOV in slice direction [mm] (default=5.0)
.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=00000000)
.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\-psize\fR: Patients size/height [mm] (default=2000.0)
.HP
\fB\-pweight\fR: Patients weight [kg] (default=50.0)
.HP
\fB\-rcname\fR: Name of receive coil (default=Unknown)
.HP
\fB\-scient\fR: Scientist Name (default=Unknown)
.HP
\fB\-sd\fR: Inter\-slice distance (from center to center) [mm] (default=10.0)
.HP
\fB\-serd\fR: Series Description (default=Unknown)
.HP
\fB\-serno\fR: Series Number (default=1)
.HP
\fB\-st\fR: Slice thickness [mm] (default=5.0)
.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=80.0)
.HP
\fB\-time\fR: Time of scan [hhmmss] (default=104558)
.HP
\fB\-tr\fR: Time between consecutive excitations [ms] (default=1000.0)
.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\-framesplit\fR: Force splitting frames with different acquisition times into separate protocol\-data pairs
.HP
\fB\-ldr\fR: If multiple LDR (labeled data record) 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 analyze asc coi dat dcm double float gz h5 hdr idx ima interfile jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit u32bit u8bit vtk xml xpro , 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 (default=0)> : Align data to the geometry (voxel locations) of an external file
.HP
\fB\-automask\fR <skip leftmost slots (default=0),dump histogram,dump histogram fit> : Create binary mask using automatic histogram\-based threshold
.HP
\fB\-cluster\fR : Create clusters of non\-zero adjacent/next\-neighbours voxels, sorted by size
.HP
\fB\-convolve\fR <convolution kernel (default=noFunction) (Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp ),full\-width\-at\-half\-maximum of kernel [mm] (default=0.0)> : Convolution in spatial dimensions
.HP
\fB\-detrend\fR <Number of low frequency components to be removed (default=5),Zero mean of resulting timecourse (default=No)> : Remove slow drift over time
.HP
\fB\-dilate\fR <radius of kernel [mm] (default=0.0)> : dilate image using spherical kernel as structuring element
.HP
\fB\-edit\fR <string in the format (timerange,slicerange,phaserange,readrange),value (default=0.0)> : Edit voxel values with range specified as single position, or 'all', or explicit range, optionally with increment (e.g. 1\-10:3)
.HP
\fB\-erode\fR <radius of kernel [mm] (default=0.0)> : erode image using spherical kernel as structuring element
.HP
\fB\-genmask\fR <lower threshold (default=0.0),upper threshold (default=0.0)> : Create binary mask including all voxels with value in given range
.HP
\fB\-inv\fR : Invert image values, i.e. lowest to highest and vice versa
.HP
\fB\-isotrop\fR <voxelsize [mm] (default=0.0)> : make image voxels isotrop through interpolation (image geometry will not change), set to zero for minimum extent
.HP
\fB\-lowpass\fR <Cut\-off frequency [Hz] (default=0.0)> : Lowpass filtering
.HP
\fB\-max\fR <Maximum value (default=0.0)> : 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 <Minimum value (default=0.0)> : Clip all values below minimum value
.HP
\fB\-minip\fR <direction (time slice phase read none )> : Perform minimum intensity projection over given direction
.HP
\fB\-noNaN\fR <Replacement value (default=0.0)> : Replaces every NaN by the given value
.HP
\fB\-nonzeromask\fR : Create binary mask including all voxels with non\-zero value
.HP
\fB\-pflip\fR : Flip data in phase direction
.HP
\fB\-prange\fR <single position, or 'all', or explicit 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 mean projection over given direction
.HP
\fB\-quantilmask\fR <quantil (default=0.0)> : Create binary mask including all voxels above the given fractional threshold
.HP
\fB\-resample\fR <new size (default=0)> : Temporal resize of image data
.HP
\fB\-resize\fR <slice\-size (default=0),phase\-size (default=0),read\-size (default=0)> : Spatial resize of image data
.HP
\fB\-reslice\fR <requested orientation (default=coronal) (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] (default=0.0),kernel size [pixel] (default=1.41421)> : In\-plane rotation
.HP
\fB\-rrange\fR <single position, or 'all', or explicit range, optionally with increment (e.g. 1\-10:3)> : Select range in read direction
.HP
\fB\-scale\fR <Slope (default=1.0),Offset (default=0.0)> : Rescale image values
.HP
\fB\-sflip\fR : Flip data in slice direction
.HP
\fB\-shift\fR <readDirection shift [pixel] (default=0.0),phaseDirection shift [pixel] (default=0.0),sliceDirection shift [pixel] (default=0.0)> : Shift data spatially
.HP
\fB\-slicetime\fR <space\-separated list of slice indices in order of acquisition> : Correct for different acquisition time points of slices
.HP
\fB\-spheremask\fR <Position string in the format (slicepos,phasepos,readpos),radius [mm] (default=0.0)> : Create binary spherical mask
.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 position, or 'all', or explicit range, optionally with increment (e.g. 1\-10:3)> : Select range in slice direction
.HP
\fB\-sum\fR <direction (time slice phase read none )> : Perform sum projection over given direction
.HP
\fB\-swapdim\fR <[rps][\-],[rps][\-],[rps][\-]> : swap/reflect/transpose dimensions by specifying a direction triple with optional reflection sign appended
.HP
\fB\-tile\fR <columns (default=0)> : Combine slices into a square 2D image
.HP
\fB\-trange\fR <single position, or 'all', or explicit range, optionally with increment (e.g. 1\-10:3)> : Select range in time direction
.HP
\fB\-tshift\fR <time shift [frames] (default=0.0)> : Shift data in time
.HP
\fB\-typemax\fR <Datatype> : Clip all values above maximum of a specific datatype
.HP
\fB\-typemin\fR <Datatype> : Clip all values below minimum of a specific datatype
.HP
\fB\-usemask\fR <filename> : Create 1D dataset including all values within binary mask from file
.SS "Supported file extensions(formats):"
.TP
3db
(Iris3D binary data)
.TP
analyze
(NIFTI/ANALYZE, dialects: fsl)
.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
h5
(ISMRMRD Image)
.TP
hdr
(Interfile, dialects: neurostat)
.TP
hdr
(NIFTI/ANALYZE, dialects: fsl)
.TP
idx
(3D\-indices of non\-zeroes in ASCII, dialects: addval)
.TP
ima
(DICOM, dialects: siemens)
.TP
interfile
(Interfile, dialects: neurostat)
.TP
jdx
(ODIN Image based on JCAMP\-DX (Joint Committee on Atomic and Molecular Physical Data))
.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 protocols based on JCAMP\-DX (Joint Committee on Atomic and Molecular Physical Data))
.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, vtkStructuredPoints)
.TP
xml
(ODIN Image based on XML (Extensible Markup Language))
.TP
xpro
(ODIN protocols based on XML (Extensible Markup Language))