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micalc
Langue: en
Version: January 2010 (ubuntu - 24/10/10)
Section: 1 (Commandes utilisateur)
Sommaire
NAME
micalc - Performs basic mathematics with data setsDESCRIPTION
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)
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