brainseg 0.0.5

A brain segmentation tool

Brain Seg

A brain segmentation tool using machine learning

Under development

This software has NOT been approved for medical analysis/diagnosis. Please use other approved software for medical use.

Models

SavedModels for use can be found at Google Drive.

Models were trained using the Mindboggle-101 data:

Klein, Arno, 2016, "Mindboggle-101 manually labeled individual brains", https://doi.org/10.7910/DVN/HMQKCK, Harvard Dataverse, V2

A Klein, SS Ghosh, FS Bao, J Giard, Y Hame, E Stavsky, N Lee, B Rossa, M Reuter, EC Neto, A Keshavan. 2017. Mindboggling morphometry of human brains. PLoS Computational Biology 13(3): e1005350. doi:10.1371/journal.pcbi.1005350 (bioRxiv 2016 preprint)

Options

positional arguments:
  filepath              Path of file to segment

optional arguments:
  -h, --help            show this help message and exit
  -s SEGMENT, --segment Segments using provided SavedModel (Directory path required)
  --segment-precision   Float32 or float64 {32,64}
  --output OUTPUT, -o   Output filepath
  --output-channels     Number of channel in output image {1,3}

Usage Examples

# Segments a sample nifti scan
$ brainseg sample.nii.gz -s sampleSavedModel -o output.nii.gz

Model Training Graphs

SavedModel_210303