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SPM.jl

Introduction

SPM.jl is a Julia package alongside the SPM software, designed for the analysis of brain imaging data sequences.

Installation

SPM.jl is available for Julia v1.6 and later releases. It can be installed with Julia built-in package manager. In a Julia session, after entering the package manager mode with ], run the command

pkg> update
pkg> add https://github.com/spm/SPM.jl

To exit from the Pkg REPL mode press the backspace key, or Ctrl + C.

SPM.jl also requires a shared library libSPM (see SPM Makefile). A compiled library libSPM.so is provided for 64-bit Linux environments.

Usage

Example of between modality coregistration using information theory (see spm_coreg.m).

If needed, you can download test data here.

julia> using SPM

julia> P1 = "./T1w.nii";

julia> P2 = "./bold.nii";

julia> x,o = SPM.Coreg.run(P1,P2,[4],"nmi")
bold.nii -> T1w.nii w. nmi, 4mm samp. & 5x5 hist. smo.
0.4885   0        0        0        0        0        | -1.0011
0.4885   0.5516   0        0        0        0        | -1.0011
0.4885   0.5516   0        0        0        0        | -1.0011
0.4885   0.5516   0        0.1212   0        0        | -1.0012
0.4885   0.5516   0        0.1212   0        0        | -1.0012
0.4885   0.5516   0        0.1212   0        0        | -1.0012
0.497    0.5516   0        0.1212   0        0        | -1.0012
0.497    0.8482   0        0.1212   0        0        | -1.0012
0.497    0.8482   0.03426  0.1212   0        0        | -1.0012
0.497    0.8482   0.03426  0.1219   0        0        | -1.0012
0.497    0.8482   0.03426  0.1219   0        0        | -1.0012
0.497    0.8482   0.03426  0.1219   0        0        | -1.0012
0.5084   1.244    0.08003  0.1227   0        0        | -1.0012
0.5084   1.244    0.08003  0.1227   0        0        | -1.0012
0.5085   1.246    0.08019  0.1227   0        0        | -1.0012
0.5085   1.246    0.08019  0.1227   0        0        | -1.0012
0.5085   1.246    0.08019  0.1227   0        0        | -1.0012
0.5085   1.246    0.08019  0.1227   0        0        | -1.0012
0.5085   1.246    0.08019  0.1227   0        0        | -1.0012
([0.5084690641189673, 1.2458319387515466, 0.08018609030614379, 0.12270502915244379, 0.0, 0.0], -1.0012251f0)

julia> A = SPM.Coreg.spm_matrix(x)
4×4 Array{Float64,2}:
 1.0   0.0       0.0       0.508469
 0.0   0.992481  0.122397  1.24583
 0.0  -0.122397  0.992481  0.0801861
 0.0   0.0       0.0       1.0