.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.2.
.TH MICALC "1" "March 2012" "micalc 1.8.5" "User Commands"
.SH NAME
micalc \-  Performs basic mathematics with data sets
.SH DESCRIPTION
micalc:  Performs basic mathematics with data sets
.IP
File formats are automatically identified by their file extension.
.SS "micalc can be used in one of the following modes:"
.IP
Binary operation with data sets and/or scalar numbers:
.IP
micalc [\-if1 <input\-file1> | \fB\-in1\fR <input\-number1>] \fB\-op\fR <operation(+,\-,*,/,lcorr,kcorr)> [\-if2 <input\-file2> | \fB\-in2\fR <input\-number1>] \fB\-of\fR <output\-file>
.IP
Accumulation of one data set:
.IP
micalc \fB\-if\fR <input\-file> \fB\-op\fR <operation(+,*)>
.IP
Transformation (magnitude, logarithm, negation, inversion, or acos) of one data set:
.IP
micalc \fB\-if\fR <input\-file> \fB\-op\fR <operation(abs,log,\-,/,acos)> \fB\-of\fR <output\-file>
.IP
Statistics of one data set:
.IP
micalc \fB\-if\fR <input\-file> [\-mean <time\-mean\-file>] [\-stdev <time\-stdev\-file>] [\-fluct <relative\-time\-stdev\-file>] [\-tcourse <average time course of all voxels>] [\-hist <histogram> \fB\-histmin\fR <minval> \fB\-histmax\fR <maxval> \fB\-histslots\fR <numofslots> \fB\-rightstairs\fR \fB\-histfract]\fR
.SS "Extra options:"
.HP
\fB\-mask\fR <Binary mask file: voxels with zeroes are discarded>
.HP
\fB\-weightmask\fR <Multiply input file(s) with this file>
.SS "File read options:"
.HP
\fB\-date\fR: Date of scan [yyyymmdd] (default=20120328yyyymmdd)
.HP
\fB\-fp\fR: FOV in phase direction [mm] (default=220.0mm)
.HP
\fB\-fr\fR: FOV in read direction [mm] (default=220.0mm)
.HP
\fB\-fs\fR: FOV in slice direction [mm] (default=5.0mm)
.HP
\fB\-nr\fR: Number of consecutive measurements (default=1)
.HP
\fB\-nx\fR: Number of points in read direction (default=128)
.HP
\fB\-ny\fR: Number of points in phase direction (default=128)
.HP
\fB\-nz\fR: Number of points in slice direction (default=1)
.HP
\fB\-pbirth\fR: Patients date of birth [yyyymmdd] (default=00000000yyyymmdd)
.HP
\fB\-pid\fR: Unique patient identifier (default=Unknown)
.HP
\fB\-pname\fR: Full patient name (default=Unknown)
.HP
\fB\-psex\fR: Patients sex (options=M F O , default=O)
.HP
\fB\-pweight\fR: Patients weight [kg] (default=50.0kg)
.HP
\fB\-scient\fR: Scientist Name (default=Unknown)
.HP
\fB\-sd\fR: Inter\-slice distance (from center to center) [mm] (default=10.0mm)
.HP
\fB\-serd\fR: Series Description (default=Unknown)
.HP
\fB\-serno\fR: Series Number (default=1)
.HP
\fB\-st\fR: Slice thickness [mm] (default=5.0mm)
.HP
\fB\-stud\fR: Study Description (default=Unknown)
.HP
\fB\-tcname\fR: Name of transmit coil (default=Unknown)
.HP
\fB\-te\fR: Time\-to\-echo of the sequence [ms] (default=80.0ms)
.HP
\fB\-time\fR: Time of scan [hhmmss] (default=165641hhmmss)
.HP
\fB\-tr\fR: Time between consecutive excitations [ms] (default=1000.0ms)
.HP
\fB\-cplx\fR: Treat data as complex and extract the given component (options=none abs pha real imag , default=none)
.HP
\fB\-ds\fR: Dataset index to extract if multiple datasets are read
.HP
\fB\-filter\fR: Read only those datasets which protocol parameter 'key' contains the string 'value' (given in the format 'key=value')
.HP
\fB\-fmap\fR: For reduced memory usage, keep filemapping after reading (raw) data, but writing into the array will result in a crash
.HP
\fB\-jdx\fR: If multiple JDX arrays are present, select this
.HP
\fB\-rdialect\fR: Read data using given dialect of the format. (default is no dialect)
.HP
\fB\-rf\fR: Read format, use it to override file extension (options=autodetect 3db asc coi dat dcm double float gz hdr idx ima jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit u32bit u8bit vtk , default=autodetect)
.HP
\fB\-skip\fR: Skip this amount of bytes before reading the raw data (default=0)
.SS "File write options:"
.HP
\fB\-append\fR: Append to existing file, only for raw data
.HP
\fB\-fnamepar\fR: Space\-separated list of protocol parameters to include when creating unique file names
.HP
\fB\-split\fR: Force splitting of protocol\-data pairs into separate files.
.HP
\fB\-type\fR: Image representation type (options=automatic float double s32bit u32bit s16bit u16bit s8bit u8bit , default=automatic)
.HP
\fB\-wdialect\fR: Write data using given dialect of the format. (default is no dialect)
.HP
\fB\-wf\fR: Write format, use it to override file extension (options=autodetect 3db asc coi dat dcm double float gz hdr idx ima jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit u32bit u8bit vtk , default=autodetect)
.HP
\fB\-wp\fR: Store the protocol separately to this file.
.SS "Filters applied to input file(s):"
.HP
\fB\-align\fR <filename,In\-plane blowup factor> : Align data to the geometry (voxel locations) of an external file
.HP
\fB\-automask\fR : Create mask using automatic histogram\-based threshold
.HP
\fB\-detrend\fR <Number of low frequency components to be removed,Zero mean of resulting timecourse> : Remove slow drift over time
.HP
\fB\-genmask\fR <lower threshold,upper threshold> : Create mask including all voxels with value in given range
.HP
\fB\-isotrop\fR <voxelsize> : make image voxels isotrop through interpolation (image geometry will not change)
.HP
\fB\-lowpass\fR <Cut\-off frequency [Hz]> : Lowpass filtering
.HP
\fB\-max\fR <Maximum value> : Clip all values above maximum value
.HP
\fB\-maxip\fR <direction (time slice phase read none )> : Perform maximum intensity projection over given direction
.HP
\fB\-merge\fR : Merge datasets into a single dataset by expanding the time dimension
.HP
\fB\-min\fR <Minumum value> : Clip all values below mininum value
.HP
\fB\-minip\fR <direction (time slice phase read none )> : Perform minimum intensity projection over given direction
.HP
\fB\-noNaN\fR <Replacement value> : Replaces every NaN by the given value
.HP
\fB\-pflip\fR : Flip data in phase direction
.HP
\fB\-prange\fR <Single value or range, optionally with increment (e.g. 1\-10:3)> : Select range in phase direction
.HP
\fB\-proj\fR <direction (time slice phase read none )> : Perform projection over given direction
.HP
\fB\-quantilmask\fR <quantil> : Create mask including all voxels above the given fractional threshold
.HP
\fB\-resample\fR <new size> : Temporal resize of image data
.HP
\fB\-resize\fR <slice\-size,phase\-size,read\-size> : Spatial resize of image data
.HP
\fB\-reslice\fR <requested orientation (sagittal coronal axial )> : reslices the image to a given orientation
.HP
\fB\-rflip\fR : Flip data in read direction
.HP
\fB\-rot\fR <angle [deg],kernel size [pixel]> : In\-plane rotation
.HP
\fB\-rrange\fR <Single value or range, optionally with increment (e.g. 1\-10:3)> : Select range in read direction
.HP
\fB\-scale\fR <Slope,Offset> : Rescale image values
.HP
\fB\-sflip\fR : Flip data in slice direction
.HP
\fB\-shift\fR <readDirection shift [pixel],phaseDirection shift [pixel],sliceDirection shift [pixel]> : Shift data spatially
.HP
\fB\-splice\fR <dimension of the data to be spliced (time slice phase read none )> : splices the image in the given direction
.HP
\fB\-srange\fR <Single value or range, optionally with increment (e.g. 1\-10:3)> : Select range in slice direction
.HP
\fB\-swapdim\fR <[rps][\-],[rps][\-],[rps][\-]> : swap/reflect dimensions by specifying a direction triple with optional reflection sign appended
.HP
\fB\-tile\fR <columns> : Combine slices into a square 2D image
.HP
\fB\-trange\fR <Single value or range, optionally with increment (e.g. 1\-10:3)> : Select range in time direction
.HP
\fB\-typemax\fR <Datatype> : Clip all values above maximum of a specific datatype
.HP
\fB\-typemin\fR <Datatype> : Clip all values below mininum of a specific datatype
.HP
\fB\-usemask\fR <filename> : Create 1D dataset including all values within mask from file
.SS "Other options:"
.HP
\fB\-v\fR <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).
.HP
\fB\-h\fR, \fB\-\-help\fR, \fB\-help\fR, \fB\-\-version\fR : Print help text or version information
.SS "Supported file extensions(formats):"
.TP
3db
(Iris3D binary data)
.TP
asc
(ASCII, dialects: tcourse )
.TP
coi
(JCAMP\-DX data sets)
.TP
dat
(Matlab ascii 2D data matrix)
.TP
dcm
(DICOM, dialects: siemens )
.TP
double
(double raw data)
.TP
float
(float raw data)
.TP
gz
(GNU\-Zip container for other formats)
.TP
hdr
(NIFTI/ANALYZE, dialects: fsl )
.TP
idx
(3D\-indices of non\-zeroes in ASCII)
.TP
ima
(DICOM, dialects: siemens )
.TP
jdx
(JCAMP\-DX image format)
.TP
mag
(DICOM, dialects: siemens )
.TP
mhd
(MetaImage)
.TP
nii
(NIFTI/ANALYZE, dialects: fsl )
.TP
ph
(DICOM, dialects: siemens )
.TP
png
(Portable Network Graphics)
.TP
pos
(x\-y positions of non\-zeroes in ASCII)
.TP
pro
(ODIN measurement protocols)
.TP
reg
(Ansoft HFSS ASCII)
.TP
s16bit
(signed 16 bit raw data)
.TP
s32bit
(signed 32 bit raw data)
.TP
s8bit
(signed 8 bit raw data)
.TP
smp
(JCAMP\-DX data sets)
.TP
u16bit
(unsigned 16 bit raw data)
.TP
u32bit
(unsigned 32 bit raw data)
.TP
u8bit
(unsigned 8 bit raw data)
.TP
vtk
(Visualization Toolkit)