Dear FreeSurfer Developers,

I seek clarification regarding a discrepancy in cerebrospinal fluid (CSF) volume measurements obtained using different FreeSurfer tools.

In my analysis, I measured CSF volume using both recon-all-clinical.sh and SAMSEG for the same subject. However, the results were significantly different:

recon-all-clinical: 236,073.36 mm³ (~236 mL)

SAMSEG: 471,854.76 mm³ (~472 mL)

Additionally, I conducted SAMSEG on 10 neurologically healthy subjects, and in all cases, the CSF volume was at least twice the normal average CSF volume (~150 mL) reported in the literature.

I would appreciate any insights into the following questions:

Why is there such a large discrepancy between the two methods?

Which method provides a more reliable estimate of total CSF volume?

Why are the estimated CSF volumes significantly higher than the known physiological average? 

Thank you for your time and assistance!

Best regards,

Nima