genmakefile(1) [debian man page]
GENMAKEFILE(1) User Commands GENMAKEFILE(1) NAME
genmakefile - Generates a Makefile for ODIN methods SYNOPSIS
genmakefile [options] <method-label> DESCRIPTION
genmakefile: Generates a Makefile for ODIN methods 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 genmakefile 1.8.5 March 2012 GENMAKEFILE(1)
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MICALC(1) User Commands MICALC(1) 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. 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(+,-,*,/,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> -histmin <minval> -histmax <maxval> -histslots <numofslots> -rightstairs -histfract] Extra options: -mask <Binary mask file: voxels with zeroes are discarded> -weightmask <Multiply input file(s) with this file> File read options: -date: Date of scan [yyyymmdd] (default=20120328yyyymmdd) -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=165641hhmmss) -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 idx ima jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit u32bit u8bit 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 -fnamepar: Space-separated list of protocol parameters to include when creating unique file names -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 idx ima jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit u32bit u8bit vtk , default=autodetect) -wp: Store the protocol separately to this file. Filters applied to input file(s): -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 -detrend <Number of low frequency components to be removed,Zero mean of resulting timecourse> : 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) -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 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 -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 -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) 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 (NIFTI/ANALYZE, dialects: fsl ) idx (3D-indices of non-zeroes in ASCII) 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) 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) vtk (Visualization Toolkit) micalc 1.8.5 March 2012 MICALC(1)