Hello,

I have two questions which I was hoping to get some help with.

(1) I was wondering whether there was a intensity threshold for grey matter and CSF. I know that Freesurfer scales the intensity so white matter has an intensity of 110 (as can be seen at the bottom of Freeviewer when I open the brianmask.mgz). I was wondering whether there is a threshold value I can use to indicate whether a voxel is part of the CSF with 100% confidence?

(2) After I make edits to my aseg output in the longitudinal stream, do I just run the following command to recreate the final volumes:

recon-long -autorecon2-noaseg -subjid <Subj_ID>

I assume the -subjid is the name of the edited time point and <Subj_ID> is the name of the recreated volumes?

Thank you,
Tamara