odin-1.8.8/0000755000175000017500000000000012415160675007471 500000000000000odin-1.8.8/cmdline-utils/0000755000175000017500000000000012415160675012242 500000000000000odin-1.8.8/cmdline-utils/micalc.10000644000175000017500000002352612370623124013475 00000000000000.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10. .TH MICALC "1" "August 2014" "micalc 1.8.8" "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. For binary operations with two input files, the protocol of the first input file will be used for the output file. .SS "micalc can be used in one of the following modes:" .IP Binary operation with data sets and/or scalar numbers: .IP micalc [\-if1 | \fB\-in1\fR ] \fB\-op\fR [\-if2 | \fB\-in2\fR ] \fB\-of\fR .IP Accumulation of one data set: .IP micalc \fB\-if\fR \fB\-op\fR .IP Transformation (magnitude, logarithm, negation, inversion, or acos) of one data set: .IP micalc \fB\-if\fR \fB\-op\fR \fB\-of\fR .IP Statistics of one data set: .IP micalc \fB\-if\fR [\-mean ] [\-stdev ] [\-fluct ] [\-tcourse ][\-hist \fB\-histslots\fR [\-histmin ] [\-histmax ] [\-rightstairs] [\-histfract] [\-loghist] ] .SS "Extra options:" .HP \fB\-mask\fR .SS "File read options:" .HP \fB\-date\fR: Date of scan [yyyymmdd] (default=20140807yyyymmdd) .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=091012hhmmss) .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 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) .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\-noscale\fR: Do not rescale values when storing integers .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 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) .HP \fB\-wp\fR: Store the protocol separately to this file. .SS "Filters applied to input file(s) and mask:" .HP \fB\-align\fR : Align data to the geometry (voxel locations) of an external file .HP \fB\-automask\fR : Create mask using automatic histogram\-based threshold .HP \fB\-cluster\fR : Create clusters of non\-zero adjacent/next\-neighbours voxels, sorted by size .HP \fB\-convolve\fR : Convolution in spatial dimensions .HP \fB\-detrend\fR : Remove slow drift over time .HP \fB\-edit\fR : Edit single voxel values .HP \fB\-genmask\fR : Create mask including all voxels with value in given range .HP \fB\-isotrop\fR : make image voxels isotrop through interpolation (image geometry will not change) .HP \fB\-lowpass\fR : Lowpass filtering .HP \fB\-max\fR : Clip all values above maximum value .HP \fB\-maxip\fR : 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 : Clip all values below mininum value .HP \fB\-minip\fR : Perform minimum intensity projection over given direction .HP \fB\-noNaN\fR : Replaces every NaN by the given value .HP \fB\-pflip\fR : Flip data in phase direction .HP \fB\-prange\fR : Select range in phase direction .HP \fB\-proj\fR : Perform mean projection over given direction .HP \fB\-quantilmask\fR : Create mask including all voxels above the given fractional threshold .HP \fB\-resample\fR : Temporal resize of image data .HP \fB\-resize\fR : Spatial resize of image data .HP \fB\-reslice\fR : reslices the image to a given orientation .HP \fB\-rflip\fR : Flip data in read direction .HP \fB\-rot\fR : In\-plane rotation .HP \fB\-rrange\fR : Select range in read direction .HP \fB\-scale\fR : Rescale image values .HP \fB\-sflip\fR : Flip data in slice direction .HP \fB\-shift\fR : Shift data spatially .HP \fB\-slicetime\fR : Correct for different acquisition time points of slices .HP \fB\-splice\fR : splices the image in the given direction .HP \fB\-srange\fR : 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 : Combine slices into a square 2D image .HP \fB\-trange\fR : Select range in time direction .HP \fB\-tshift\fR