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