miconv: Converts medical image data between formats.
File formats are automatically identified by their file extension.
usage: miconv [options] <input-file> [<output-file>]
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:
-fx: FOV in read direction [mm] (default=220.0mm)
-fy: FOV in phase direction [mm] (default=220.0mm)
-nr: Number of consecutive measurements (default=1)
-nx: Spatial resolution in read direction (default=128)
-ny: Spatial resolution in phase direction (default=128)
-pbirth: Patients date of birth in <year><mont><day> (default=19730913)
-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: TransmitCoil Name (default=Unknown)
-te: Time-to-echo of the sequence [ms] (default=80.0ms)
-tr: Time between consecutive excitations [ms] (default=1000.0ms)
File read options:
-abs: Treat data as complex and extract magnitude
-dir: Try to combine multiple files found in directory
-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')
-jdx: If multiple JDX arrays are present, select this
-pha: Treat data as complex and extract the phase
-rdialect: Read data using given dialect of the format. (default is no dialect)
-rf: Read format, use it to override file extension (options=autodetect asc coi dat dcm double float gz hdr ima img jdx mag mhd nii ph pos 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: Split protocol-data pairs into separate files. "%a" (if given in the name) will be replaced by the seriesnumber and its description.
-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 asc coi dat dcm double float gz hdr ima img jdx mag mhd nii ph pos s16bit s32bit s8bit smp u16bit u32bit u8bit v vtk , default=autodetect)
-wp: Store the protocol separately to this file."%a" (if given in the name) will be replaced by the seriesnumber and its description.
Filters:
-max <Maximum value> : Clip all values above maximum value
-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> : reslices the image to have a given orientation if necessary
-rflip : Flip data in read direction
-rot <Rotate by this angle> : 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
-srange <Single value or range, optionally with increment (e.g. 1-10:3)> : Select range in slice direction
-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
Other options:
-v <loglevel> or <component:loglevel> for debugging/tracing all components or a sinlge component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog), 4(significantDebug), 5(normalDebug), 6(verboseDebug).
Supported file extensions(formats):
asc (ASCII)
coi (JCAMP-DX data sets)
dat (Matlab ascii 2D data matrix)
dcm (DICOM)
double (double raw data)
float (float raw data)
gz (GNU-Zip container for other formats)
hdr (ANALYZE)
ima (DICOM)
img (ANALYZE)
jdx (JCAMP-DX image format)
mag (DICOM)
mhd (MetaImage)
nii (NIFTI, dialects: fsl )
ph (DICOM)
pos (x-y positions of non-zeroes in 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 xlipsia )
vtk (Visualization Toolkit)
miconv -rf dcm -dir mosaic mosaic.nii
Converting a short (16 bit) raw data file '2dseq' of size 256x256 to a DICOM file 'image.dcm':
miconv -nx 256 -ny 256 -rf short 2dseq image.dcm
Extracting the data from the 2nd slice (index 1) of Vista file 'image.v' and store it in new Vista file 'slice1.v':
miconv -srange 1 image.v slice1.v
1.5.1