Fibers.jl

Julia package for reconstructing fiber trajectories from multi-scale, multi-modal imaging data
Author lincbrain
Popularity
16 Stars
Updated Last
10 Months Ago
Started In
March 2022

Build Status

Load this package

If you want julia (and this package) to use multi-threading for faster computation, you have to explicitly tell it to. You can do that either by starting julia with julia --thread auto, or by setting the environment variable JULIA_NUM_THREADS to auto before starting julia. (This will use the total number of CPU threads available on your computer. Alternatively, you can specify a number of threads in place of auto.)

julia> using Fibers

Read .mgh, .mgz, .nii, .nii.gz volumes

julia> aa = mri_read("/usr/local/freesurfer/dev/subjects/fsaverage/mri/aparc+aseg.mgz");

julia> fa = mri_read("/usr/local/freesurfer/dev/trctrain/hcp/MGH35_HCP_FA_template.nii.gz");

Display volume and header summary info in the terminal

julia> disp(aa)

julia> disp(fa)

Display a slice view of the volume in a pop-up window

By default this will be an axial view, middle slice, first frame. See ?fs.show for how to change what is displayed.

julia> show(aa)

julia> show(fa)

Write .mgh, .mgz, .nii, .nii.gz volumes

julia> mri_write(aa, "/tmp/aparc+aseg.nii.gz")

julia> mri_write(fa, "/tmp/MGH35_HCP_FA_template.mgz")

Read Bruker scan directories

julia> ph = mri_read("/opt/nmrdata/PV-7.0.0/ayendiki/Phantom.cO1/5/");

Read a .trk tractography streamline file

julia> tr = trk_read("/usr/local/freesurfer/dev/trctrain/hcp/mgh_1001/syn/acomm.bbr.prep.trk");

Write a .trk tractography streamline file

julia> trk_write(tr, "/tmp/acomm.trk")

Tutorial

A gentle introduction to diffusion MRI

Acknowledgements

Development of this package is supported by the NIH National Institute of Neurologic Disorders and Stroke (grants UM1-NS132358, R01-NS119911, R01-NS127353).