Hello Freesurfer developers,

I am trying to measure the optic chiasm volume from a set of subjects and I ran recon-all with Freesurfer version 7.1.1 to do that. I also ran HCP minimal processing pipeline on the same set of subjects for some other project and I believe that pipeline runs Freesurfer v6 before it does the additional HCP related processing. When I compare the optic chiasm volume from these two Freesurfer runs, the results appear to be quite different. I believe Freesurfer 6 version is more accurate as it correlates better with some other metrics I have. I have a few questions:

1 – I want to systematically check the analysis results step by step to see where it might have gone wrong, but I don’t really know where to start. The initial Tailarach registrations look okay and I don’t really see anything wrong with the processed volume and surface images. What other quality checks can I perform on the data to catch the source of this discrepancy in the results?

2 – I also ran the thalamic segmentation script with Freesurfer 7 to measure the LGN volumes. Now these results look pretty correlated with the other biometric measurements I have so that the results look sensible to me. However, I got a bit worried that the issue that affects the optic chiasm results might also be influencing the LGN results. Is this a possibility? How much does this segmentation script depend on the intermediate recon-all files such as transformation matrices and what not?

3 – Finally, can I use the thalamic segmentation script on the recon-all output generated by version 6 or does it depend on any new files/methods introduced by version 7 recon-all?

Best,

Ozzy