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micalc

NAME

micalc - Performs basic mathematics with data sets

DESCRIPTION

micalc: Performs basic mathematics with data sets

File formats are automatically identified by their file extension.

Usage:

Binary operation with data sets and/or scalar numbers:

micalc [-if1 <input-file1> | -in1 <input-number1>] -op <operation(+,-,*,/,lcorr,kcorr)> [-if2 <input-file2> | -in2 <input-number1>] -of <output-file>

Accumulation of one data set:

micalc -if <input-file> -op <operation(+,*)>

Transformation (magnitude, logarithm, negation, inversion, or acos) of one data set:

micalc -if <input-file> -op <operation(abs,log,-,/,acos)> -of <output-file>

Statistics of one data set:

micalc -if <input-file> [-mean <time-mean-file>] [-stdev <time-stdev-file>] [-fluct <relative-time-stdev-file>] [-tcourse <time-course of all voxels>] [-hist <histogram> -histmin <minval> -histmax <maxval> -histslots <numofslots> -rightstairs -histfract]

Extra options:

-mask <Mask for data>

File read 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=122058hhmmss)

-tr: Time between consecutive excitations [ms] (default=1000.0ms)

-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 applied to input files:

-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)