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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.

   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.

       -nv: be less verbose, show progress in percent only

       -p: Load this protcol for defaults

   Protocol options:
       -date: Date of scan [yyyymmdd] (default=20100109yyyymmdd)

       -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=122056hhmmss)

       -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  asc  coi dat dcm double float gz hdr ima jdx mag mhd nii ph
              png pos reg s16bit s32bit s8bit smp u16bit u32bit u8bit v vtk  ,
              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

       -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 asc coi dat dcm double float gz hdr ima
              jdx mag mhd nii ph png pos reg s16bit s32bit  s8bit  smp  u16bit
              u32bit u8bit v vtk , 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

       -detrend <Number of low frequency components to be  removed>  :  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)

       -max <Maximum value> : Clip all values above maximum value

       -merge  :  Merge  datasets  into a single dataset by expanding the time
              dimension

       -min <Minumum value> : Clip all values below mininum value

       -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

       -resize <slice-size,phase-size,read-size> : Resize 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 dimension

       -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 using 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),         4(significantDebug),         5(normalDebug),
              6(verboseDebug).

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

   Supported file extensions(formats):
       3db    (Iris3D binary data)

       asc    (ASCII)

       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 )

       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)

       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)

       v      (Vista, dialects: common odin lipsia )

       vtk    (Visualization Toolkit)