VolProc ~ MP2RAGE Volume Processor

Requirements

• Properly defined parameters file in JSON format (cf. example.json)

Runtime dependencies

• libboost_timer.so.1.83.0 (Boost Timer shared library to measure performance / elapsed time)

Usage

• Install Boost-1.83.0 on your system, or download the shared library file libboost_timer.so.1.83.0 in the Releases section and move it to your /usr/local/lib directory.
• Run the executable while providing the path to your JSON configuration file in the command line:

{ROOTDIR}/bin/main {ROOTDIR}/example.json

This is a header-only library so integrating it to existing C++ code should be as trivial as adding an #include to the proper header files (assuming the source dependencies are met).

Hard-coded choices in code base

• No extrapolation: points beyond interpolant's definition are set to 0.
• Propagation of the extrapolation mask to derived volumes except for Synthetic EDGE and its denoised version
• Geometric linear interpolation from a Delaunay triangulation mesh as $(B_1, : T_1\text{-w UNI}) \rightarrow qT_1$ interpolator
• No rescaling of inputs in interpolator
• $qT_1$ and time quantities are expected to be given in $ms$ for synthetic volume computation to play well
• All volumes are rounded to nearest integer before export to NIfTI format
• $qR_1$ is given in per kilosecond ($ks^{-1}$) to limit information loss when rounding to nearest integer
• Outputs are given in:
  • $qT_1$ $\rightarrow$ $ms$
  • $qR_1$ $\rightarrow$ $ks^{-1}$
  • if use_deprecated_normalization_from_12bits: true:
    • $B_1$-corrected $T_1$-w UNI $\rightarrow$ $[0, : 4096]$
    • Synthetic EDGE $\rightarrow$ $[0, : 4096]$
    • Synthetic FLAWS $\rightarrow$ $[0, : 4096]$
    • Denoised $T_1$-w UNI $\rightarrow$ $[0, : 4096]$
    • Denoised $B_1$-corrected $T_1$-w UNI $\rightarrow$ $[0, : 4096]$
    • Denoised Synthetic EDGE $\rightarrow$ $[0, : 4096]$
    • Denoised Synthetic FLAWS $\rightarrow$ $[0, : 4096]$
  • else if use_deprecated_normalization_from_12bits: false:
    • $B_1$-corrected $T_1$-w UNI $\rightarrow$ $[0, : 4095]$
    • Synthetic EDGE $\rightarrow$ $[0, : 4095]$
    • Synthetic FLAWS $\rightarrow$ $[0, : 4095]$
    • Denoised $T_1$-w UNI $\rightarrow$ $[0, : 4095]$
    • Denoised $B_1$-corrected $T_1$-w UNI $\rightarrow$ $[0, : 4095]$
    • Denoised Synthetic EDGE $\rightarrow$ $[0, : 4095]$
    • Denoised Synthetic FLAWS $\rightarrow$ $[0, : 4095]$
• Denoising of ... uses ... range for denoising algorithm:
  • $T_1$-w UNI $\rightarrow$ $[-0.5, : 0.5]$
  • $B_1$-corrected $T_1$-w UNI $\rightarrow$ $[-0.5, : 0.5]$
  • if use_denoising_on_unit_normed_synthetic_maps: true:
    • Synthetic EDGE $\rightarrow$ $[-0.5, : 0.5]$
    • Synthetic FLAWS $\rightarrow$ $[-0.5, : 0.5]$
  • else if use_denoising_on_unit_normed_synthetic_maps: false:
    • if use_deprecated_normalization_from_12bits: true:
      • Synthetic EDGE $\rightarrow$ $[0, : 4096]$
      • Synthetic FLAWS $\rightarrow$ $[0, : 4096]$
    • else if use_deprecated_normalization_from_12bits: false:
      • Synthetic EDGE $\rightarrow$ $[0, : 4095]$
      • Synthetic FLAWS $\rightarrow$ $[0, : 4095]$

Features included

• MP2RAGE bijectivity's correction
• $qT_1$ computation
• $qR_1$ computation
• $B_1$-corrected $T_1$-w UNI computation
• Synthetic EDGE computation
• Synthetic FLAWS computation
• Masking outside valid $qT_1$ range for volumes derived from $qT_1$
• Normalization from/to DICOM 12bits range, unit cube ([-0.5, 0.5]), various units
• In-house denoising Algorithms
• ANTs' volume transformation to reference (e.g. bringing $B_1$ to $T_1$-w UNI space)
• ANTs' Gaussian smoothing
• Various utilities, templating and overloads
• Multithreading

Still needs

• Fix boost's timer library static linking (#1)
• Proper CMakeLists.txt / Makefile with support for tests / release / debug / example (#2)
• Test suite (support for windows / linux) (#3)
• Documentation (#4)
• Copyright and Credits header in files (#5)
• README / Wiki (#4, #6)

Misc

Compilation dependencies

• C++ $\geq$ 17
• Boost (https://github.com/boostorg/boost)
• Eigen3 (https://gitlab.com/libeigen/eigen)
• ANTs (https://github.com/ANTsX/ANTs)
• RNifti (https://github.com/jonclayden/RNifti)
• libinterpolate (https://github.com/CD3/libInterpolate)
• gnuplot / gnuplot-iostream
• make / g++

Tested for exact reproduction of previous code

• $qT_1$
• $qR_1$
• $B_1$-corrected $T_1$-w UNI
• $B_1$-corrected $T_1$-w UNI denoised
• $T_1$-w UNI denoised
• Synthetic EDGE
• Synthetic EDGE denoised
• Synthetic FLAWS
• Synthetic FLAWS denoised

Future

• GUI?
• @amasliash's synthetic EDGE / synthetic FLAWS parameters optimizer?