Reading and writing structural neuroimaging file formats for Java.
File format readers and writers for file formats used in structural neuroimaging research, with a focus on the surface-based workflow used in FreeSurfer.
- Meshes:
- Read brain meshes in FreeSurfer binary mesh format (like recon_all output file
<SUBJECTS_DIR>/<subject>/surf/lh.white): use functionFsSurface.fromFsSurfaceFile() - Read meshes from MZ3 format, as used by Surf-Ice
- Write in PLY, OBJ, and FreeSurfer binary mesh formats:
FsSurface.writeToFile() - Read meshes from PLY format files (ASCII type)
- Read brain meshes in FreeSurfer binary mesh format (like recon_all output file
- Labels (FreeSurfer volume and surface labels, like
<subject>/label/lh.cortex.label):- Read from FreeSurfer label format:
FsLabel.fromFsLabelFile() - Write in FreeSurfer label format and to CSV format:
FsLabel.writeToFile()
- Read from FreeSurfer label format:
- Annots or mesh parcellations (like Desikan atlas parcellation in recon_all output file
<SUBJECTS_DIR>/<subject>/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()
- Read from FreeSurfer annot format:
- Brain volumes (3D or 4D MRI scans, like
<subject>/mri/brain.mgz):- Read from files in FreeSurfer MGH format:
FsMgh.fromFsMghFile() - Read from files in FreeSurfer MGZ format:
FsMgh.fromFsMgzFile()
- Read from files in FreeSurfer MGH format:
- 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
<subject>/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.
This is work-in-progress, not yet. We will upload to Maven central once it's ready.
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.
The unit tests also include various usage examples.
Development information can be found here.