I have been attempting to analyze a group of subjects through the longitudinal TRACULA pipeline and have run into many issues regarding the preprocessing step making use of the thalamic segmentation. I've combed through the archives on this topic and have found many different threads relating to issues with the necessary files for the thalamic segmentation not being created, particularly the aparc+aseg+thalnuc.nii.gz file during the trac-all -prep step.

I am attempting these analyses on a newer Mac Studio computer and cannot make use of the MATLAB 2014b runtime to segment the thalamus with the old script. Using the suggestions from this previous question, I ran the segment_subregions thalamus python script and renamed all the outputs to match the MATLAB outputs (ThalamicNuclei.v12.T1.FSvoxelSpace.mgz, ThalamicNuclei.v12.T1.mgz, ThalamicNuclei.v12.T1.volumes.txt), but still ran into errors with the prep script and creation of the aparc+aseg+thalnuc.nii.gz file mentioned above.

It seems like all the previous threads on this issue result in no permanent solution, are there any suggestions on ways to fix this, at least temporarily? Any discussion on this topic would be appreciated. I've also attached the log files from one of my failed runs, as well as the TRACULA configuration file. This was all done on Freesurfer 7.4.1.