dipy_math#

Synopsis#

Perform mathematical operations on volume input files.

This workflow allows the user to perform mathematical operations on multiple input files. e.g. to add two volumes together, subtract one: dipy_math "vol1 + vol2 - vol3" t1.nii.gz t1_a.nii.gz t1_b.nii.gz The input files must be in Nifti format and have the same shape.

Usage#

dipy_math [OPTIONS] operation input_files

Input Parameters#

  • operation

    Mathematical operation to perform. supported operators are:

    • Bitwise operators (and, or, not, xor): &, |, ~, ^

    • Comparison operators: <, <=, ==, !=, >=, >

    • Unary arithmetic operators: -

    • Binary arithmetic operators: +, -, *, /, **, <<, >>

    Supported functions are:

    • where(bool, number1, number2) -> number: number1 if the bool condition is true, number2 otherwise.

    • {sin,cos,tan}(float|complex) -> float|complex: trigonometric sine, cosine or tangent.

    • {arcsin,arccos,arctan}(float|complex) -> float|complex: trigonometric inverse sine, cosine or tangent.

    • arctan2(float1, float2) -> float: trigonometric inverse tangent of float1/float2.

    • {sinh,cosh,tanh}(float|complex) -> float|complex: hyperbolic sine, cosine or tangent.

    • {arcsinh,arccosh,arctanh}(float|complex) -> float|complex: hyperbolic inverse sine, cosine or tangent.

    • {log,log10,log1p}(float|complex) -> float|complex: natural, base-10 and log(1+x) logarithms.

    • {exp,expm1}(float|complex) -> float|complex: exponential and exponential minus one.

    • sqrt(float|complex) -> float|complex: square root.

    • abs(float|complex) -> float|complex: absolute value.

    • conj(complex) -> complex: conjugate value.

    • {real,imag}(complex) -> float: real or imaginary part of complex.

    • complex(float, float) -> complex: complex from real and imaginary parts.

    • contains(np.str, np.str) -> bool: returns True for every string in op1 that contains op2.

  • input_files

    Any number of Nifti1 files

General Options#

  • --dtype

    Data type of the resulting file. (default: None)

Output Options#

  • --out_dir

    Output directory (default: current directory)

  • --out_file

    Name of the resulting file to be saved. (default: math_out.nii.gz)

References#

Garyfallidis, E., M. Brett, B. Amirbekian, A. Rokem, S. Van Der Walt, M. Descoteaux, and I. Nimmo-Smith. Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics, 1-18, 2014.

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