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MICONV(1) User Commands MICONV(1)

NAME

miconv - Converts medical image data between formats.

SYNOPSIS

miconv [ options] <input-file> [<output-file>]

DESCRIPTION

miconv: Converts medical image data between formats.
File formats are automatically identified by their file extension. It expects at least two filenames/directories (for the input and output file) at the end of the command line. An exception is the option '-l' which requires only one filename/directory to list its content.

General options:

-l: Lists space-separated set of protocol parameters and exits. Use '-l help' to get a list of possible parameters and '-l all' to list all parameters. The parameter 'output-file' must be omitted when using this option.
-p: Load this protcol for defaults

Protocol 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=128)
-ny: Number of points in phase direction (default=128)
-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=091009hhmmss)
-tr: Time between consecutive excitations [ms] (default=1000.0ms)

File read options:

-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)

File write options:

-append: Append to existing file, only for raw data
-fnamepar: Space-separated list of protocol parameters to include when creating unique file names
-noscale: Do not rescale values when storing integers
-split: Force splitting of protocol-data pairs into separate files.
-type: Image representation type (options=automatic float double s32bit u32bit s16bit u16bit s8bit u8bit , default=automatic)
-wdialect: Write data using given dialect of the format. (default is no dialect)
-wf: Write 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)
-wp: Store the protocol separately to this file.

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

Other options:

-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).
-h, --help, -help, --version : Print help text or version information

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)
August 2014 miconv 1.8.8