MINC2 for Julia

using Minc2
using StatsBase

# read volume from minc file, represent it as array of doubles (Float64 in julia world)
icbm=Minc2.read_volume("mni_icbm152_t1_tal_nlin_sym_09c.mnc", store=Float64)
@show mean(Minc2.array(icbm))

using Minc2
using StatsBase

# read T1w scan
icbm=Minc2.read_volume("mni_icbm152_t1_tal_nlin_sym_09c.mnc", store=Float64)
# read label mask, represent it as array of bytes 
lab=Minc2.read_volume("mni_icbm152_cls_tal_nlin_sym_09c.mnc", store=UInt8)

# calculate image statistics per label
for (i,l) in [1=>"CSF",2=>"GM",3=>"WM"]
    println("$(l):$(mean(Minc2.array(icbm)[ Minc2.array(lab).==i ]))")
end

using Minc2

# read T1w scan
icbm=Minc2.read_volume("mni_icbm152_t1_tal_nlin_sym_09c.mnc", store=Float64)

# read transformation
tfm=Minc2.load_transforms("rotate.xfm")

# apply transformation to the volume
transformed_icbm=Minc2.resample_volume(icbm; tfm, order=2, fill=0.0)

# write the resulting volume into file, append history
# the resulting volume will be stored with unsigned short minc data type
# but will preserve floating point vales used fixe-point arithmetics
Minc2.save_volume("transformed_icbm.mnc",transformed_icbm, store=UInt16, history="Julia example")

using Minc2

# read ROI labels
rois = Minc2.read_volume("rois.mnc", store=UInt8)

# calculate voxel volume 
start, step, dir_cos = Minc2.decompose(Minc2.voxel_to_world(rois))
voxel_volume = abs(reduce(*,step,init=1))

# read transformation
tfm = Minc2.load_transforms("nonlinear.xfm")

# define sampling parameters for jacobian field
jacobians = Minc2.empty_volume_like(lab, store=Float64)

# calculate per-voxel jacobians
Minc2.calculate_jacobian!(tfm, jacobians)

# Integrate per ROI
for (i,l) in [1=>"ROI-1",2=>"ROI-2",3=>"ROI-3"]
    println("$(l):$( sum((Minc2.array(rois) .== i) .* Minc2.array(jac) )*voxel_volume)")
end

using CairoMakie
using Minc2

# read T1w scan
icbm=Minc2.read_volume("mni_icbm152_t1_tal_nlin_sym_09c.mnc", store=Float64)
# read label mask, represent it as array of bytes 
lab=Minc2.read_volume("mni_icbm152_cls_tal_nlin_sym_09c.mnc", store=UInt8)


fig = Figure()
gc = fig[1, 1] = GridLayout()

Minc2.draw_outline_with_labels(gc, icbm, lab, 
    labels=Dict([1=>"CSF",2=>"GM",3=>"WM"]),
    nslices = 5)

resize_to_layout!(fig)

save("mni_icbm152_segmentation.png", fig, px_per_unit = 1)

using CairoMakie
using Minc2

# read T1w scan
anat=Minc2.read_volume("mni_icbm152_t1_tal_nlin_sym_09c.mnc",store=Float64)
# read field
gm=Minc2.read_volume("mni_icbm152_gm_tal_nlin_sym_09c.mnc",store=Float64)

fig = Figure()
gc = fig[1, 1] = GridLayout()

# set background to transparent
Minc2.array(gm)[Minc2.array(gm) .< 1e-6] .= NaN

Minc2.draw_outline_with_heatmap(gc, anat, gm, 
    heat_limits=(0.0,1.0),cmap=:turbo,
    nslices = 5)

resize_to_layout!(fig)

save("mni_icbm152_gm.png", fig, px_per_unit = 1)