miconv - Online in the Cloud

PROGRAM:

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)

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