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>] [-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=20090930yyyymmdd)
-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=153257hhmmss)
-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)
micalc -if1 image1.dcm -op '-' -if2 image2.dcm -of diff.float
Multiply image magnitude of Vista file 'image.v' by a factor 10:
micalc -if1 image.v -op '*' -in2 10 -of image.v
Accumulate all values in file 'image.float' and write result to console:
micalc -if image.float -op '+'
Negate values (invert sign) of file image.hdr and write result to neg.hdr
micalc -if image.hdr -op '-' neg.hdr
Print statistics about file 'data.asc' to console:
micalc -if data.asc
Write time-course mean and fluctuation (relative standard deviation over time) of file 'tcourse.v' to file 'mean.v' and 'stdev.v', respectively:
micalc -if tcourse.v -mean mean.v -fluct stdev.v
Calculate histogram in interval (0.0,100.0) with 64 steps of DICOMs in directory cbv:
micalc -if cbv -hist histogram.asc -histmin 0.0 -histmax 100.0 -histslots 64
Please note that it might be necessary to quote the operation argument (as shown above) in order to prevent the shell from expanding it.
1.5.6