xenial (1) micalc.1.gz

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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.  For binary operations with two
              input files, the protocol of the first input file will be used for the output file.

   micalc can be used in one of the following modes:
              Binary operation with data sets and/or scalar numbers:

              micalc [-if1 <input-file1> | -in1  <input-number1>]  -op  <operation(+,-,*,/,min,max,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 <average  time  course  of  all  voxels>][-hist  <histogram>
              -histslots  <numofslots>  [-histmin  <minval>]  [-histmax  <maxval>]  [-rightstairs]  [-histfract]
              [-loghist] ]

   Extra options:
       -mask <Binary mask file: voxels with zeroes are discarded>

   File read 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=091012hhmmss)

       -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 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 applied to input file(s) and mask:
       -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)