https://github.com/dfsp-spirit/neuro

Go module for reading and writing structural neuroimaging file formats. Supports FreeSurfer MGH, MGZ, and related formats.
https://github.com/dfsp-spirit/neuro

biomedical brain fileformats freesurfer go golang mri mri-images neuroimaging neuroscience

Last synced: 3 days ago
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Go module for reading and writing structural neuroimaging file formats. Supports FreeSurfer MGH, MGZ, and related formats.

• Host: GitHub
• URL: https://github.com/dfsp-spirit/neuro
• Owner: dfsp-spirit
• License: mit
• Created: 2023-05-30T19:08:52.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2024-04-23T16:00:06.000Z (8 months ago)
• Last Synced: 2024-10-31T18:12:06.804Z (about 2 months ago)
• Topics: biomedical, brain, fileformats, freesurfer, go, golang, mri, mri-images, neuroimaging, neuroscience
• Language: Go
• Homepage:
• Size: 8.02 MB
• Stars: 2
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGES
  • License: LICENSE

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README

        
# neuro

Go module for reading and writing structural neuroimaging file formats. Supports FreeSurfer MGH, MGZ, and related formats.

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[![GoDoc](https://godoc.org/github.com/dfsp-spirit/neuro?status.svg)](https://godoc.org/github.com/dfsp-spirit/neuro) [![license](https://img.shields.io/github/license/dfsp-spirit/neuro.svg)](https://github.com/dfsp-spirit/neuro/blob/main/LICENSE)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8126957.svg)](https://doi.org/10.5281/zenodo.8126957)

## About

This repo contains a very early version of a [Go](https://go.dev/) module for reading structural neuroimaging file formats. Currently supported formats include:

* [FreeSurfer](https://freesurfer.net) brain surface format: a triangular mesh file format. Used for recon-all output files like `/surf/lh.white`.

    - Read file format (function `ReadFsSurface`) into `Mesh` data structure.

    - Export `Mesh` to PLY, STL, OBJ formats.

    - Computation of basic `Mesh` properties (vertex and face count, bounding box, average edge length, total surface area, ...).

* FreeSurfer curv format: stores per-vertex data (also known as a brain overlay), e.g., cortical thickness at each vertex of the brain mesh. Typically used for native space data for a single subject, for recon-all output files like `/surf/lh.thickness`.

    - Read file format (function `ReadFsCurv`)

    - Write file format (function `WriteFsCurv`)

    - Export data to JSON format.

* FreeSurfer MGH and MGZ formats: store 3-dimensional or 4-dimensional (subject/time dimension) magnetic resonance imaging (MRI) scans of the human brain (e.g., `/mri/brain.mgz`). Can also be used to store per-vertex data, including multi-subject data on a common brain template like fsaverage (e.g., files like `/surf/lh.thickness.fwhm5.fsaverage.mgh`). The MGZ format is just gzip-compressed MGH format.

    - Read MGH format (function `ReadFsMgh`)

    - Read MGZ format (function `ReadFsMgh`), without the need to manually decompress first. The function handles both MGH and MGZ.

    - Full header information is available, so the image orientation can be reconstructed from the RAS information.

* FreeSurfer label format: these files store labels, i.e., extra information for a subset of the vertices of a mesh or the voxels of a volume. Sometimes per-vertex or per-voxel data is stored in the labels data field, but in other case the relevant information is simply whether or not a certain element (voxel, vertex) is part of the label. Used for recon-all output files like `/label/lh.cortex.label`.

    - Read ASCII label format (function `ReadFsLabel`)

    - See also the related utility function `VertexIsPartOfLabel`

![Vis](./lhwhite.jpg?raw=true "Visualization of the demo brain mesh.")

## Usage

### Installation

```shell

go get github.com/dfsp-spirit/neuro

```

### Full Documentation including usage examples for functions

The full documentation can be found on the central go documentation page at [pkg.go.dev](https://pkg.go.dev/github.com/dfsp-spirit/neuro#section-documentation).

It includes the full API documentation and usage examples for the functions.

### Complete demo applications

Demo applications that use `neuro` are available in the [cmd/](./cmd/) directory:

* A command line app that reads a FreeSurfer mesh and prints some mesh information, like total surface area, average edgle length, etc: [example_surface.go](./cmd/example_surface/example_surface.go)

* A command line app that reads per-vertex cortical thickness data from a FreeSurfer curv file and exports it to a JSON file: [example_curv.go](./cmd/example_curv/example_curv.go)

* A command line app that reads a three-dimensional human brain scan (MRI image) from a FreeSurfer MGH file and prints some header data and the value of a voxel: [example_mgh.go](./cmd/example_mgh/example_mgh.go)

* A command line app that reads a label from a FreeSurfer surface label file and optionally exports the label data to JSON format: [example_label.go](./cmd/example_label/example_label.go)

## Developer information

Please see the [Developer information](./README_DEV.md) if you want to compile and run the demo apps, unit tests, and similar things.

## Author, License and Getting Help

The `neuro` module for Go was written by [Tim Schäfer](https://ts.rcmd.org).

It is free software, published under the very permissive [MIT license](./LICENSE).

Note that this library is **not** a part of FreeSurfer, and it is **in no way** endorsed by the FreeSurfer developers. Please do not contact them regarding this library, especially not for support. [Open an issue](https://github.com/dfsp-spirit/neuro/issues) in this repo instead.