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

Reading and writing structural neuroimaging file formats for Java.
https://github.com/dfsp-spirit/jneuroformats

brain fileformats java mri neuroimaging

Last synced: 7 days ago
JSON representation

Reading and writing structural neuroimaging file formats for Java.

• Host: GitHub
• URL: https://github.com/dfsp-spirit/jneuroformats
• Owner: dfsp-spirit
• License: mit
• Created: 2023-07-17T09:04:38.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2023-10-02T12:59:24.000Z (about 1 year ago)
• Last Synced: 2024-05-01T15:39:55.785Z (6 months ago)
• Topics: brain, fileformats, java, mri, neuroimaging
• Language: Java
• Homepage:
• Size: 8.11 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGES
  • License: LICENSE

Awesome Lists containing this project

README

        
# jneuroformats

Reading and writing structural neuroimaging file formats for Java.

[![main](https://github.com/dfsp-spirit/jneuroFormats/actions/workflows/unittests.yml/badge.svg?branch=main)](https://github.com/dfsp-spirit/jneuroFormats/actions)

## About

File format readers and writers for file formats used in structural neuroimaging research, with a focus on the

surface-based workflow used in [FreeSurfer](https://freesurfer.net).

![Vis](./img/rgl_brain_aparc.jpg?raw=true "An aparc brain atlas visualization.")

## Features

* Meshes:

  - Read brain meshes in FreeSurfer binary mesh format (like recon_all output file `//surf/lh.white`): use function `FsSurface.fromFsSurfaceFile()`

  - Read meshes from MZ3 format, as used by [Surf-Ice](https://github.com/neurolabusc/surf-ice)

  - Write in PLY, OBJ, and FreeSurfer binary mesh formats: `FsSurface.writeToFile()`

  - Read meshes from PLY format files (ASCII type)

* Labels (FreeSurfer volume and surface labels, like `/label/lh.cortex.label`):

  - Read from FreeSurfer label format:  `FsLabel.fromFsLabelFile()`

  - Write in FreeSurfer label format and to CSV format: `FsLabel.writeToFile()`

* Annots or mesh parcellations (like Desikan atlas parcellation in recon_all output file `//label/lh.aparc.annot`):

  - Read from FreeSurfer annot format: `FsAnnot.fromFsAnnotFile()`

  - Write to FreeSurfer annot format and to CSV (including the color table):  `FsAnnot.writeToFile()`

* Brain volumes (3D or 4D MRI scans, like `/mri/brain.mgz`):

  - Read from files in FreeSurfer MGH format: `FsMgh.fromFsMghFile()`

  - Read from files in FreeSurfer MGZ format: `FsMgh.fromFsMgzFile()`

* Per-Vertex data and per-voxel data, like cortical thickness or statistical results:

  - Read from MGH/MGZ files (they can store 4D arrays, which is useful for the raw images and per-vertex/per-voxel data)

  - Read from MZ3 files: `Mz3.fromMz3File()`. Can also read per-vertex colors from MZ3 files.

  - Read from FreeSurfer curv files (like `/surf/lh.thickness`): `FsCurv.fromFsCurvFile()`

  - Write to FreeSurfer curv files: `FsCurv.writeToFile()`

Many of the classes provide utility methods which are typically needed in structural neuroimaging, so check the API documentation before re-inventing the wheel. Examples include the function `FsAnnot.getVertexColorsRgb()` to compute the vertex colors for a brain atlas from the annotation labels and its color map.

## Installation

This is work-in-progress, not yet. We will upload to Maven central once it's ready.

## Documentation and Usage

The API documentation will be published to a central repository once the package is officially released. See the development information if you want to generate it yourself.

A full example app can be found in the file [App.java](./jneuroformats/src/main/java/org/rcmd/jneuroformats/App.java).

The [unit tests](./jneuroformats/src/test/java/org/rcmd/jneuroformats/) also include various usage examples.

## Development

Development information can be found [here](./jneuroformats/README_dev.md).