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

• git clone https://github.com/thalamicseg/thomas.git
• Extract THOMAS-priors.zip to thomas/
• python require.py

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