ROMEO

calculateweights(wrapped; weights=:romeo, kwargs...)

Calculates weights for all edges. size(weights) == [3, size(wrapped)...]

Optional keyword arguments:

• weights: Options are [:romeo] | :romeo2 | :romeo3 | :bestpath.
• mag: Additional mag weights are used.
• mask: Unwrapping is only performed inside the mask.
• phase2: A second reference phase image (possibly with different echo time). It is used for calculating the phasecoherence weight.
• TEs: The echo times of the phase and the phase2 images as a tuple (eg. (5, 10) or [5, 10]).

unwrap(wrapped::AbstractArray; keyargs...)

ROMEO unwrapping for 3D and 4D data.

Optional keyword arguments:

• TEs: Required for 4D data. The echo times for multi-echo data. In the case of single-echo application with phase and the phase2 as a tuple (eg. (5, 10) or [5, 10]).
• weights: Options are [:romeo] | :romeo2 | :romeo3 | :bestpath.
• mag: The magnitude is used to improve the unwrapping-path.
• mask: Unwrapping is only performed inside the mask.
• phase2: A second reference phase image (possibly with different echo time). It is used for calculating the phasecoherence weight. This is automatically done for 4D multi-echo input and therefore not required.
• correctglobal=false: If true corrects global n2π offsets.
• individual=false: If true perform individual unwrapping of echos. Type ?unwrap_individual for more information
• template=1: echo that is spatially unwrapped (if individual is false)
• maxseeds=1: higher values allow more seperate regions
• merge_regions=false: spatially merge neighboring regions after unwrapping
• correct_regions=false: bring each regions median closest to 0 by adding n2π
• wrap_addition=0: [0;π], allows 'linear unwrapping', neighbors can have more (π+wrap_addition) phase difference
• temporal_uncertain_unwrapping=0.5: Useful for veins. It uses spatial unwrapping on voxels that have high uncertainty values after temporal unwrapping. A higher quality threshold re-unwraps more voxels spatially.

Examples

julia> using MriResearchTools
julia> phase = readphase("phase_3echo.nii")
julia> unwrapped = unwrap(phase; TEs=[1,2,3])
julia> savenii(unwrapped, "unwrapped.nii"; header=header(phase))

unwrap(wrapped::AbstractArray; keyargs...)

ROMEO unwrapping for 3D and 4D data.

Optional keyword arguments:

• TEs: Required for 4D data. The echo times for multi-echo data. In the case of single-echo application with phase and the phase2 as a tuple (eg. (5, 10) or [5, 10]).
• weights: Options are [:romeo] | :romeo2 | :romeo3 | :bestpath.
• mag: The magnitude is used to improve the unwrapping-path.
• mask: Unwrapping is only performed inside the mask.
• phase2: A second reference phase image (possibly with different echo time). It is used for calculating the phasecoherence weight. This is automatically done for 4D multi-echo input and therefore not required.
• correctglobal=false: If true corrects global n2π offsets.
• individual=false: If true perform individual unwrapping of echos. Type ?unwrap_individual for more information
• template=1: echo that is spatially unwrapped (if individual is false)
• maxseeds=1: higher values allow more seperate regions
• merge_regions=false: spatially merge neighboring regions after unwrapping
• correct_regions=false: bring each regions median closest to 0 by adding n2π
• wrap_addition=0: [0;π], allows 'linear unwrapping', neighbors can have more (π+wrap_addition) phase difference
• temporal_uncertain_unwrapping=0.5: Useful for veins. It uses spatial unwrapping on voxels that have high uncertainty values after temporal unwrapping. A higher quality threshold re-unwraps more voxels spatially.

Examples

julia> using MriResearchTools
julia> phase = readphase("phase_3echo.nii")
julia> unwrapped = unwrap(phase; TEs=[1,2,3])
julia> savenii(unwrapped, "unwrapped.nii"; header=header(phase))

unwrap_individual(wrapped::AbstractArray{T,4}; TEs, keyargs...) where T

Performs individual unwrapping of the echoes instead of temporal unwrapping. Still uses multi-echo information to improve the quality map. This function is identical to unwrap with the flag individual=true. The syntax is identical to unwrap, but doesn't support the temporal_uncertain_unwrapping and template options: Base.Docs.DocStr(svec(" unwrap(wrapped::AbstractArray; keyargs...)\n\nROMEO unwrapping for 3D and 4D data.\n\n### Optional keyword arguments:\n\n- TEs: Required for 4D data. The echo times for multi-echo data. In the case of single-echo \n application with phase and the phase2 as a tuple (eg. (5, 10) or [5, 10]).\n- weights: Options are [:romeo] | :romeo2 | :romeo3 | :bestpath.\n- mag: The magnitude is used to improve the unwrapping-path.\n- mask: Unwrapping is only performed inside the mask.\n- phase2: A second reference phase image (possibly with different echo time).\n It is used for calculating the phasecoherence weight. This is automatically\n done for 4D multi-echo input and therefore not required.\n- correctglobal=false: If true corrects global n2π offsets.\n- individual=false: If true perform individual unwrapping of echos.\n Type ?unwrap_individual for more information\n- template=1: echo that is spatially unwrapped (if individual is false)\n- maxseeds=1: higher values allow more seperate regions\n- merge_regions=false: spatially merge neighboring regions after unwrapping\n- correct_regions=false: bring each regions median closest to 0 by adding n2π\n- wrap_addition=0: [0;π], allows 'linear unwrapping', neighbors can have more\n (π+wrapaddition) phase difference\n- `temporaluncertainunwrapping=0.5: Useful for veins. It uses spatial\n unwrapping on voxels that have high uncertainty values after temporal\n unwrapping. A higher quality threshold re-unwraps more voxels spatially.\n\n# Examples\n``julia-repl\njulia> using MriResearchTools\njulia> phase = readphase(\"phase3echo.nii\")\njulia> unwrapped = unwrap(phase; TEs=[1,2,3])\njulia> savenii(unwrapped, \"unwrapped.nii\"; header=header(phase))\n\n"), unwrap(wrapped::AbstractArray; keyargs...)

ROMEO unwrapping for 3D and 4D data.

### Optional keyword arguments:

  * `TEs`: Required for 4D data. The echo times for multi-echo data. In the case of single-echo    application with phase and the phase2 as a tuple (eg. (5, 10) or [5, 10]).
  * `weights`: Options are [`:romeo`] | `:romeo2` | `:romeo3` | `:bestpath`.
  * `mag`: The magnitude is used to improve the unwrapping-path.
  * `mask`: Unwrapping is only performed inside the mask.
  * `phase2`: A second reference phase image (possibly with different echo time).   It is used for calculating the phasecoherence weight. This is automatically   done for 4D multi-echo input and therefore not required.
  * `correctglobal=false`: If `true` corrects global n2π offsets.
  * `individual=false`: If `true` perform individual unwrapping of echos.   Type `?unwrap_individual` for more information
  * `template=1`: echo that is spatially unwrapped (if `individual` is `false`)
  * `maxseeds=1`: higher values allow more seperate regions
  * `merge_regions=false`: spatially merge neighboring regions after unwrapping
  * `correct_regions=false`: bring each regions median closest to 0 by adding n2π
  * `wrap_addition=0`: [0;π], allows 'linear unwrapping', neighbors can have more   (π+wrap_addition) phase difference
  * `temporal_uncertain_unwrapping=0.5`: Useful for veins. It uses spatial   unwrapping on voxels that have high uncertainty values after temporal   unwrapping. A higher quality threshold re-unwraps more voxels spatially.

# Examples

julia-repl julia> using MriResearchTools julia> phase = readphase("phase_3echo.nii") julia> unwrapped = unwrap(phase; TEs=[1,2,3]) julia> savenii(unwrapped, "unwrapped.nii"; header=header(phase)) ``` , Dict{Symbol, Any}(:typesig => Union{}, :module => ROMEO, :linenumber => 28, :binding => ROMEO.unwrap!, :path => "/home/runner/work/ROMEO.jl/ROMEO.jl/src/unwrapping.jl"))

unwrap_individual(wrapped::AbstractArray{T,4}; TEs, keyargs...) where T

Performs individual unwrapping of the echoes instead of temporal unwrapping. Still uses multi-echo information to improve the quality map. This function is identical to unwrap with the flag individual=true. The syntax is identical to unwrap, but doesn't support the temporal_uncertain_unwrapping and template options: Base.Docs.DocStr(svec(" unwrap(wrapped::AbstractArray; keyargs...)\n\nROMEO unwrapping for 3D and 4D data.\n\n### Optional keyword arguments:\n\n- TEs: Required for 4D data. The echo times for multi-echo data. In the case of single-echo \n application with phase and the phase2 as a tuple (eg. (5, 10) or [5, 10]).\n- weights: Options are [:romeo] | :romeo2 | :romeo3 | :bestpath.\n- mag: The magnitude is used to improve the unwrapping-path.\n- mask: Unwrapping is only performed inside the mask.\n- phase2: A second reference phase image (possibly with different echo time).\n It is used for calculating the phasecoherence weight. This is automatically\n done for 4D multi-echo input and therefore not required.\n- correctglobal=false: If true corrects global n2π offsets.\n- individual=false: If true perform individual unwrapping of echos.\n Type ?unwrap_individual for more information\n- template=1: echo that is spatially unwrapped (if individual is false)\n- maxseeds=1: higher values allow more seperate regions\n- merge_regions=false: spatially merge neighboring regions after unwrapping\n- correct_regions=false: bring each regions median closest to 0 by adding n2π\n- wrap_addition=0: [0;π], allows 'linear unwrapping', neighbors can have more\n (π+wrapaddition) phase difference\n- `temporaluncertainunwrapping=0.5: Useful for veins. It uses spatial\n unwrapping on voxels that have high uncertainty values after temporal\n unwrapping. A higher quality threshold re-unwraps more voxels spatially.\n\n# Examples\n``julia-repl\njulia> using MriResearchTools\njulia> phase = readphase(\"phase3echo.nii\")\njulia> unwrapped = unwrap(phase; TEs=[1,2,3])\njulia> savenii(unwrapped, \"unwrapped.nii\"; header=header(phase))\n\n"), unwrap(wrapped::AbstractArray; keyargs...)

ROMEO unwrapping for 3D and 4D data.

### Optional keyword arguments:

  * `TEs`: Required for 4D data. The echo times for multi-echo data. In the case of single-echo    application with phase and the phase2 as a tuple (eg. (5, 10) or [5, 10]).
  * `weights`: Options are [`:romeo`] | `:romeo2` | `:romeo3` | `:bestpath`.
  * `mag`: The magnitude is used to improve the unwrapping-path.
  * `mask`: Unwrapping is only performed inside the mask.
  * `phase2`: A second reference phase image (possibly with different echo time).   It is used for calculating the phasecoherence weight. This is automatically   done for 4D multi-echo input and therefore not required.
  * `correctglobal=false`: If `true` corrects global n2π offsets.
  * `individual=false`: If `true` perform individual unwrapping of echos.   Type `?unwrap_individual` for more information
  * `template=1`: echo that is spatially unwrapped (if `individual` is `false`)
  * `maxseeds=1`: higher values allow more seperate regions
  * `merge_regions=false`: spatially merge neighboring regions after unwrapping
  * `correct_regions=false`: bring each regions median closest to 0 by adding n2π
  * `wrap_addition=0`: [0;π], allows 'linear unwrapping', neighbors can have more   (π+wrap_addition) phase difference
  * `temporal_uncertain_unwrapping=0.5`: Useful for veins. It uses spatial   unwrapping on voxels that have high uncertainty values after temporal   unwrapping. A higher quality threshold re-unwraps more voxels spatially.

# Examples

julia-repl julia> using MriResearchTools julia> phase = readphase("phase_3echo.nii") julia> unwrapped = unwrap(phase; TEs=[1,2,3]) julia> savenii(unwrapped, "unwrapped.nii"; header=header(phase)) ``` , Dict{Symbol, Any}(:typesig => Union{}, :module => ROMEO, :linenumber => 28, :binding => ROMEO.unwrap!, :path => "/home/runner/work/ROMEO.jl/ROMEO.jl/src/unwrapping.jl"))

voxelquality(phase::AbstractArray; keyargs...)

Calculates a quality for each voxel. The voxel quality can be used to create a mask. The quality range is [0;1]

Examples

julia> qmap = voxelquality(phase_3echo; TEs=[1,2,3]);
julia> mask = robustmask(qmap);

Takes the same inputs as romeo/unwrap: Base.Docs.DocStr(svec(" unwrap(wrapped::AbstractArray; keyargs...)\n\nROMEO unwrapping for 3D and 4D data.\n\n### Optional keyword arguments:\n\n- TEs: Required for 4D data. The echo times for multi-echo data. In the case of single-echo \n application with phase and the phase2 as a tuple (eg. (5, 10) or [5, 10]).\n- weights: Options are [:romeo] | :romeo2 | :romeo3 | :bestpath.\n- mag: The magnitude is used to improve the unwrapping-path.\n- mask: Unwrapping is only performed inside the mask.\n- phase2: A second reference phase image (possibly with different echo time).\n It is used for calculating the phasecoherence weight. This is automatically\n done for 4D multi-echo input and therefore not required.\n- correctglobal=false: If true corrects global n2π offsets.\n- individual=false: If true perform individual unwrapping of echos.\n Type ?unwrap_individual for more information\n- template=1: echo that is spatially unwrapped (if individual is false)\n- maxseeds=1: higher values allow more seperate regions\n- merge_regions=false: spatially merge neighboring regions after unwrapping\n- correct_regions=false: bring each regions median closest to 0 by adding n2π\n- wrap_addition=0: [0;π], allows 'linear unwrapping', neighbors can have more\n (π+wrapaddition) phase difference\n- `temporaluncertainunwrapping=0.5: Useful for veins. It uses spatial\n unwrapping on voxels that have high uncertainty values after temporal\n unwrapping. A higher quality threshold re-unwraps more voxels spatially.\n\n# Examples\n``julia-repl\njulia> using MriResearchTools\njulia> phase = readphase(\"phase3echo.nii\")\njulia> unwrapped = unwrap(phase; TEs=[1,2,3])\njulia> savenii(unwrapped, \"unwrapped.nii\"; header=header(phase))\n\n"), unwrap(wrapped::AbstractArray; keyargs...)

ROMEO unwrapping for 3D and 4D data.

### Optional keyword arguments:

  * `TEs`: Required for 4D data. The echo times for multi-echo data. In the case of single-echo    application with phase and the phase2 as a tuple (eg. (5, 10) or [5, 10]).
  * `weights`: Options are [`:romeo`] | `:romeo2` | `:romeo3` | `:bestpath`.
  * `mag`: The magnitude is used to improve the unwrapping-path.
  * `mask`: Unwrapping is only performed inside the mask.
  * `phase2`: A second reference phase image (possibly with different echo time).   It is used for calculating the phasecoherence weight. This is automatically   done for 4D multi-echo input and therefore not required.
  * `correctglobal=false`: If `true` corrects global n2π offsets.
  * `individual=false`: If `true` perform individual unwrapping of echos.   Type `?unwrap_individual` for more information
  * `template=1`: echo that is spatially unwrapped (if `individual` is `false`)
  * `maxseeds=1`: higher values allow more seperate regions
  * `merge_regions=false`: spatially merge neighboring regions after unwrapping
  * `correct_regions=false`: bring each regions median closest to 0 by adding n2π
  * `wrap_addition=0`: [0;π], allows 'linear unwrapping', neighbors can have more   (π+wrap_addition) phase difference
  * `temporal_uncertain_unwrapping=0.5`: Useful for veins. It uses spatial   unwrapping on voxels that have high uncertainty values after temporal   unwrapping. A higher quality threshold re-unwraps more voxels spatially.

# Examples

julia-repl julia> using MriResearchTools julia> phase = readphase("phase_3echo.nii") julia> unwrapped = unwrap(phase; TEs=[1,2,3]) julia> savenii(unwrapped, "unwrapped.nii"; header=header(phase)) ``` , Dict{Symbol, Any}(:typesig => Union{}, :module => ROMEO, :linenumber => 28, :binding => ROMEO.unwrap!, :path => "/home/runner/work/ROMEO.jl/ROMEO.jl/src/unwrapping.jl"))

See also unwrap