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THOMAS: Thalamus-Optimized Multi-Atlas Segmentation

Segmentation of the thalamus into 12 nuclei using the white-matter-nulled image contrast and PICSL's joint label fusion. Note that this requires priors/ provided elsewhere.

Please see the new version of this project here, which implements STTHOMAS and provides priors/.

Requirements

  • ANTs
    • NOTE: before April 2016, there was a bug in ANTs/Examples/antsJointFusion.cxx when using the "-x" switch, please rebuild ANTs from the latest source to fix this.
  • FSL
  • convert3d

Installation

Usage

  • python THOMAS_v0.py -h
  • Example: python THOMAS_v0.py -p 4 --tempdir ants --jointfusion image.nii.gz ./ ALL
    • tempdir is often useful in case something goes wrong, you can resume from previous attempts.
    • jointfusion calls the original implementation of the PICSL MALF algorithm instead of antsJointFusion. This was used in the publication.
  • swapdimlike.py - reorients an image to match the orientation of another
  • form_multiatlas.py - combines many independent labels together into a single atlas