neuroformats

Handling of structural neuroimaging file formats for Rust.

The neuroformats crate provides access to structural neuroimaging data in Rust by implementing parsers for various file formats. The focus is on surface-based brain morphometry data, as produced from 3D MRI images by tools like FreeSurfer, CAT12 and others.

Installation

The neuroformats crate is on crates.io.

To use the library in your project, add it as a dependency in your Cargo.toml file, e.g.:

[dependencies]
neuroformats = "0.2.3"

Features

• Read and write FreeSurfer per-vertex data in curv format (like subject/surf/lh.thickness): functions neuroformats::read_curv and write_curv
• Read and write brain meshes in FreeSurfer binary mesh format (like subject/surf/lh.white): read_surf and write_surf
• Read and write FreeSurfer label files (like subject/label/lh.cortex.label): read_label and write_label
• Read FreeSurfer brain surface parcellations (like subject/label/lh.aparc.annot): read_annot
• Read and write FreeSurfer brain volumes and other data from MGH and MGZ files: read_mgh and write_mgh

Various utility functions are implemented for performing common computations on the returned structs, e.g. computing the vox2ras matrix from the MGH header data or finding all vertices in a brain surface parcellation that belong to a certain brain atlas region.

Documentation

API docs

The neuroformats API docs can be found at docs.rs/neuroformats.

Usage example

Read vertex-wise cortical thickness computed by FreeSurfer:

use neuroformats::read_curv;
let curv = read_curv("subjects_dir/subject1/surf/lh.thickness").unwrap();
let thickness_at_vertex_0 : f32 = curv.data[0];

You now have a Vec<f32> with the cortical thickness values in curv.data. The order of the values matches the vertex order of the respective brain surface reconstruction (e.g., the white surface mesh of the left brain hemisphere in subjects_dir/subject1/surf/lh.white).

See the neuroformats API docs and the unit tests in the source code for more examples.

Development

Unit tests and continuous integration

Continuous integration results:

Travis CI under Linux

LICENSE

The neuroformats crate is free software, dual-licensed under the MIT or APACHE-2 licenses.

Contributions

Contributions are very welcome. Please get in touch before making major changes to avoid wasted effort.

Help and contact

If you want to discuss something, need help or found a bug, please open an issue here on Github.

The neuroformats crate was written by Tim Schäfer. You can find my email address on my website if you need to contact me.