[Freesurfer] segmentHA_T2 newbie questions

External Email - Use Caution

Hi,

Trying to run the HippoAmig segmentation with T1-w and T2-w files for the first time and I have a few basic questions I could not resolve looking on the FS wiki:

1. Does the T2-w image need to be first recon-all processed like the T1-w?

On the wiki the command line is: segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1

2. Does “bert” correspond to the directory for recon-all subject “bert” after been processed?

3. Does the FILE_ADDITIONAL_SCAN need to be a nit scan or should it point to the freesurfer directory post recon-all (this is kind of related to question #1 I realize).

4. In ANALYSIS_IS can I type just “T2”?

Thanks!

K