High level functions for operations on MRI scans

3D Volume information

Minc2.voxel_to_world — Function

voxel_to_world(grid::GridTransform)

Extract voxel to world affine transform from a GridTransform

grid - GridTransform

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voxel_to_world(grid::InverseGridTransform)

Extract voxel to world affine transform from a InverseGridTransform

grid - InverseGridTransform

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voxel_to_world(hdr::MincHeader)::AffineTransform{Float64}

Give AffineTransform for world to voxel transformation based on header

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voxel_to_world(h::VolumeHandle,ijk::Vector{Float64})::Vector{Float64}

Convert contignuous 0-based voxel indexes (I,J,K) to world coordinates (X,Y,Z) 0-based

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voxel_to_world(vol::Volume3D)

Extract voxel to world affine transform from a Volume3D

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Minc2.world_to_voxel — Function

world_to_voxel(grid::GridTransform)

Extract world to voxel affine transform from a GridTransform

grid - GridTransform

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world_to_voxel(grid::InverseGridTransform)

Extract world to voxel affine transform from a InverseGridTransform

grid - InverseGridTransform

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world_to_voxel(h::VolumeHandle, xyz::Vector{Float64})::Vector{Float64}

Convert world coordinates (X,Y,Z) to contignuous voxel indexes (I,J,K) 0-based

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world_to_voxel(hdr::MincHeader)::AffineTransform{Float64}

Give AffineTransform for voxel to world transformation

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world_to_voxel(vol::Volume3D)

Extract world to voxel affine transform from a Volume3D

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Minc2.array — Function

array(grid::GridTransform)

Extract underlying plain array

grid - GridTransform

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array(grid::InverseGridTransform)

Extract underlying plain array

grid - InverseGridTransform

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array(vol::Volume3D)

Extract underlying plain array

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Minc2.history — Function

history(vol::Volume3D)

Extract history metadata

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File IO functions

Loading 3D volumes

Minc2.read_volume — Function

read_volume(fn::String; store::Type{T}=Float64)::Volume3D{T}

Read Volume3D from minc file

fn - filename
store - underlying array type

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Minc2.read_nifti_volume — Function

read_nifti_volume(fn::AbstractString; store::Type{T}=Float64)::Volume3D{T}

Read Volume3D from .nii or .nii.gz file

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Saving 3D volumes

Minc2.save_volume — Function

save_volume(fn::AbstractString, 
    vol::Volume3D{T,N}; 
    store::Type{S}=Float32,
    history=nothing)

Save Volume3D to minc file

fn - filename
vol - Volume3D to save
store - underlying MINC data type, to be used for storage

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Minc2.save_nifti_volume — Function

save_nifti_volume(fn::AbstractString, vol::Volume3D{T}; 
    store::Type{S}=Float32, history=nothing)

Save Volume3D into .nii or .nii.gz file

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Loading transformations

Minc2.read_transforms — Function

read_transforms(fname::String)::Vector{AnyTransform}

Read transformations from .xfm file fname

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Minc2.read_itk_nifti_transform — Function

read_itk_nifti_transform(fn::AbstractString;
    store::Type{T}=Float32)::Minc2.GridTransform{Float64,T}

Read ANTs style warp transform

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Minc2.read_ants_transform — Function

read_ants_transform(fn::AbstractString; store::Type{T}=Float32)::Minc2.AnyTransform

Read .txt and .nii(.nii.gz) transforms produces by ANTs

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Saving transformations

Minc2.save_transforms — Function

save_transforms(fname::String, 
    xfm::Union{Vector{XFM}, XFM};
    grid_store::Type{T}=Float32 ) where {T, XFM<:AnyTransform}

Save transformations into .xfm file,

Arguments

fname: output file name
xfm: vector of transformations to save, or a single transformation
grid_store: type of storage for grid files (default: Float32)

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Minc2.save_itk_nifti_transform — Function

save_itk_nifti_transform(fn::AbstractString,
    xfm::Minc2.GridTransform{Float64,T}; store::Type{S}=Float32)

Write ANTs style warp transform

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Minc2.save_itk_txt_transform — Function

save_itk_txt_transform(fn::AbstractString,
    xfm::Minc2.AffineTransform{Float64})

Write affine transform in ITK .txt format

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3D Volume creation

Minc2.Volume3D — Type

Volume3D{T,N}

An abstract 3D volume, could be vector field or volume with time dimension

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Minc2.empty_volume_like — Function

empty_volume_like(
        fn::String; 
        store::Type{T}=Float64, history=nothing)::Volume3D{T}

Create an empty Volume3D

fn - filename of a minc file that is used for sampling information
store - underlying array type

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empty_volume_like(
    vol::Volume3D{T1,N}; 
    store::Type{T}=Float64, 
    history=nothing)

Create an empty Volume3D

vol - Volume3D that is used for sampling information
store - underlying array type
history - minc history

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Minc2.full_volume_like — Function

full_volume_like(
        fn::String,
        fill::T=zero(T); 
        store::Type{T}=Float64, history=nothing)::Volume3D{T}

Create an empty Volume3D

fn - filename of a minc file that is used for sampling information
store - underlying array type

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full_volume_like(
    vol::Volume3D{T1,N}; 
    store::Type{T}=Float64, 
    history=nothing)

Create an empty Volume3D

vol - Volume3D that is used for sampling information
store - underlying array type
history - minc history

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3D Volume manipulations

Minc2.resample_volume — Function

resample_volume(
    in_vol::Volume3D{T,3};
    like::Union{Volume3D{O,3},Nothing}=nothing,
    tfm::Union{Vector{XFM},XFM,Nothing}=nothing, 
    itfm::Union{Vector{XFM},XFM,Nothing}=nothing, 
    interp::I=nothing, 
    fill=0.0,
    order=1,
    ftol=1.0/80,
    max_iter=10)::Volume3D

Resample Volume3D using transformation

in_vol - input Volume3D
like - Volume3D that is used for sampling information
itfm - inverse of the transformation to apply (i.e from output to input)
tfm - transformation to apply (i.e from output to input) (instead of itfm)
interp - interpolation method
fill - fill value
ftol - tolerance, for inverse transformations
max_iter - maximum number of iterations, for inverse transformations

Equivalent to mincresample minc command

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Minc2.resample_volume! — Function

resample_volume!(in_vol::AbstractArray{T,3}, 
    out_vol::AbstractArray{T,3}, 
    v2w::AffineTransform{C}, 
    w2v::AffineTransform{C}, 
    itfm::Union{Vector{XFM},XFM};
    interp::I=BSpline(Quadratic(Line(OnCell()))),
    fill=0.0,
    ftol=1.0/80,
    max_iter=10)

Resample 3D array using transformation

in_vol - input 3D array
out_vol - output 3D array
v2w - voxel to world affine transform in the output array
w2v - world to voxel affine transform in the input array
itfm - inverse of the transformation to apply (i.e from output to input)
interp - interpolation method
fill - fill value
ftol - tolerance, for inverse transformations
max_iter - maximum number of iterations, for inverse transformations

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resample_volume!(
    in_vol::Volume3D{T,3}, 
    out_vol::Volume3D{O,3}; 
    tfm::Union{Vector{XFM},XFM,Nothing}=nothing, 
    itfm::Union{Vector{XFM},XFM,Nothing}=nothing, 
    interp::I=nothing, 
    fill=0.0, 
    order=nothing,
    ftol=1.0/80,
    max_iter=10)::Volume3D{O,3}

Resample Volume3D using transformation

in_vol - input Volume3D
out_vol - output Volume3D
itfm - inverse of the transformation to apply (i.e from output to input)
tfm - transformation to apply (i.e from output to input) (instead of itfm)
interp - interpolation method
fill - fill value
ftol - tolerance, for inverse transformations
max_iter - maximum number of iterations, for inverse transformations

Equivalent to mincresample minc command

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Minc2.resample_grid — Function

resample_grid(
    in_grid::Volume3D{T,4}, 
    itfm::Union{Vector{XFM}, XFM}; 
    like::Union{Nothing,Volume3D{L,4}}=nothing)::Volume3D{T,4}

Resample Volume3D that contain 4D array, using transformation, assume 1st dimension is non spatial

in_grid - input Volume3D with 4D array describing vector field
itfm - inverse of the transformation to apply (i.e from output to input)
like - Volume3D that is used for sampling information

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Minc2.resample_grid! — Function

resample_grid!(
    in_grid::Volume3D{T,4},
    out_grid::Volume3D{T,4},
    itfm::Union{Vector{XFM}, XFM}=nothing)::Volume3D{T,4}

Resample Volume3D that contain 4D array, using transformation, assume 1st dimension is non spatial

in_grid - input Volume3D with 4D array describing vector field
out_grid - output Volume3D with 4D array describing vector field
itfm - inverse of the transformation to apply (i.e from output to input)

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Minc2.crop_volume — Function

crop_volume(in_vol::Volume3D{T,N},crop;
    fill_val::T=zero(T))::Volume3D{T,N}

Crop (or pad) a volume

in_vol - input Volume3D
crop - crop specification for each direction, e.g. [(10,10),(20,20),(5,10)] , negative values mean padding

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3D Volume and geometrical transformation link

Minc2.calculate_jacobian — Function

calculate_jacobian(
    tfm::Union{Vector{XFM},XFM};
    like::Volume3D{T,3}; 
    interp::I=BSpline(Quadratic(Line(OnCell()))),
    ftol=1.0/80,
    max_iter=10)::Volume3D{T,3}

Calculate dense jacobian determinant field for an arbitrary transformation

tfm - transformation to use
out_vol - output Volume3D
interp - interpolation method
ftol - tolerance, for inverse transformations
max_iter - maximum number of iterations, for inverse transformations

Roughly equivalent to mincblob minc command

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Minc2.calculate_jacobian! — Function

calculate_jacobian!(
    tfm::Union{Vector{XFM},XFM},
    out_vol::AbstractArray{T,3},
    out_v2w::AffineTransform{C};
    interp::I=BSpline(Quadratic(Line(OnCell()))),
    ftol=1.0/80,
    max_iter=10)

Calculate dense jacobian determinant field for an arbitrary transformation

tfm - transformation to use
out_vol - output 3D array
out_v2w - voxel to world affine transform in the output array
interp - interpolation method
ftol - tolerance, for inverse transformations
max_iter - maximum number of iterations, for inverse transformations

Roughly equivalent to mincblob minc command

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calculate_jacobian!(
    tfm::Union{Vector{XFM},XFM}, 
    out_vol::Volume3D{T,3}; 
    interp::I=BSpline(Quadratic(Line(OnCell()))),
    ftol=1.0/80,
    max_iter=10)::Volume3D{T,3}

Calculate dense jacobian determinant field for an arbitrary transformation

tfm - transformation to use
out_vol - output Volume3D
interp - interpolation method
ftol - tolerance, for inverse transformations
max_iter - maximum number of iterations, for inverse transformations

Roughly equivalent to mincblob minc command

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Missing docstring.

Missing docstring for Minc2.GridTransform. Check Documenter's build log for details.

Missing docstring.

Missing docstring for Minc2.InverseGridTransform. Check Documenter's build log for details.

Minc2.tfm_to_grid — Function

tfm_to_grid(
    tfm::Union{Vector{XFM}, XFM},
    ref::G;
    store::Type{T}=Float64,ftol=1.0/80,max_iter=10)::Volume3D{T,4}

Convert arbitrary transformation into Volume3D with 4D array containing vector field

tfm - transformation to use
v2w - voxel to world affine transform in the output array
ftol - tolerance, for inverse transformations
max_iter - maximum number of iterations, for inverse transformations

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Minc2.normalize_tfm — Function

normalize_tfm(tfm::Union{Vector{XFM}, XFM},
    ref::G;
    store::Type{T}=Float64,ftol=1.0/80,max_iter=10)::GridTransform{Float64,T}

Convert arbitrary transformation into a single GridTransform

tfm - transformation to use
ref - GridTransform that is used for sampling information
store - underlying array type
ftol - tolerance, for inverse transformations
max_iter - maximum number of iterations, for inverse transformations

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normalize_tfm(tfm::Union{Vector{XFM}, XFM},
    ref::G;
    store::Type{T}=Float64,ftol=1.0/80,max_iter=10)::GridTransform{Float64,T}

Convert arbitrary transformation into a single GridTransform

tfm - transformation to use
ref - Volume3D that is used for sampling information
store - underlying array type
ftol - tolerance, for inverse transformations
max_iter - maximum number of iterations, for inverse transformations

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