Dear Freesurfer users,

Sorry for reposting this message again, but I really need your help.

We have downloaded the Freesurfer 6.0 version since we are really interested in the brainstem segmentation. We are working with a pc equipped with a 3.6 GHz CPU and 16 GB RAM. We installed freesurfer6.0 on a virtual machine Linux (CentOs 6.7) enabling 4vcpu 11Gb of RAM. Disk space was 50 GB and after installation we have 15 GB free for data.

We have launched recon-all –all for some cases and everything went right. Then we have tried to launch recon-all –all –s nameofsunbject –brainstem-structures and the process, after about 6 hours, stacks, during the SegmentSubject process and after having computing hyperparameters for estimation of Gaussian parameters. Do you have any ideas of what is happening?

We tried to launch the brainstem segmentation also for the test data ( ftp://surfer.nmr.mgh.harvard.edu/pub/data/hipposubfields-testdata.tgz) but we still have the same problem.

Could it be a problem the use of a virtual machine Linux instead of real Linux machine?

Thank you for your help.

Riccardo Gubellini