Hi Octavian

1. just untar it to a difference place and point FREESURFER_HOME there and you should be fine without deleting 5.2.

2. Not sure. Zeke? Nick?

3. Andre (ccd) can point you at them. We find that the FLAIR version of T2_SPACE is best, but it works without the inversion as well.

cheers Bruce

On Tue, 12 Nov 2013, Octavian Lie wrote:

Dear All,   We use freesurfer in an automatic routine mainly for brain extraction/ parcellation schemes. I want to upgrade from 5.2 to 5.3 on a linux (ubuntu, 64bit) computer, but without surprises. So:

1. When extracting files/installing freesurfer tar.gz, would the update override the

5.2 files if I want to keep the same path, or I have to delete 5.2 first? I obviously want to preserve '/subjects' data already processed. 2. Freesurfer distribution contains some CUDA files. On the computer, I have CUDA 5.5 version. Do you see any incompatibility issues (5.2 worked ok in this respect). 3. Could you send me the T1 and T2 space MR protocols you use for assistance with getting pial recon optimized.   Thank you,    Octavian