Hello,
I’m recreating the pipeline from the paper (https://onlinelibrary.wiley.com/doi/10.1002/epi.70099) and am currently attempting to combine Lausanne and THOAMS parcellations, but can’t seem to find some crucial files in the repository ( GitHub - roryjpiper/thalamus_dMRI_epilepsy: Tractography and structural connectivity processing pipeline · GitHub ). The 6_connectome.sh script uses labelconvert with label lookup files (Scale1_old_thomas_labels.txt, Scale1_new_thomas_labels.txt, and thalamus equivalents) and these are missing from the repository.
I’ve contacted the author and have received no response yet. Has anyone used this pipeline and has access to these files, or knows how to reconstruct them from the Lausanne and THOMAS label sets?
For reference, my Lausanne labels are standard FreeSurfer integers (2-255 subcortical, 1000-2035 cortical) and my THOMAS left hemisphere labels are integers 2-14 corresponding to AV, VA, VLa, VLP, VPL, Pul, LGN, MGN, CM, MD-Pf, Hb, MTT.
Thanks