xenial (1) miconv.1.gz

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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.  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)