Hi FreeSurfer List I have been running Freesurfer for some time now and I want to calculate brain structure volumes of all the subjects. I used the command " mri_segstats --seg aseg.mgz --ctab-default --sum out.sum" within the subject's mri directory to get the volume segmentation results from the out.sum file. I want to calculate total brain volume with and without the cerebellum, volumes of total gray and white matter, sub-cortical gray matter objects such as Putaman and Caudate, the volumes of white matter structures such as CC and the volume of the Thalamus. I searched through the earlier postings and found a lot of information regarding this matter. However, due to overwhelming ideas, suggestions and some were very old, I am now kind of confused with the correct method to follow. So, I appreciate if freesurfer expert could help me with following questions, 1. Is above command and the resulting out.sum file, the correct method to use? 2. If not ,what is the best methods and commands that I should use to get above volumes 3. Is the volume under the name "Unknown" the total brain volume with or without the cerebellum. 4. What is the best way to get the inter cranial volume ? 5. Why there are zero volumes under the Left-Thalamus or right-Thalamus ?
Please forgive me if this is a repetition of a previous posting. Thank you in advance
Truly, Indika Walimuni Research Associate University of Texas Health Science Center Houston, TX.