Hi Miracle,

I believe Doug (CCed) ran into a similar problem recently, and I think the problem had to do with mixing versions.

What exact version are you using?

Cheers,

/Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <miracooloz@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 30 May 2018 at 16:11
To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution

Hello,

I am using v6.0 installed on a linux server (via PUTTY) to segment hippocampal subfields. I downloaded the runtime from this link (https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the instructions on how to install it ( it was installed on the same server as v6.0). The installation process worked fine.

However, when I wanted to run recon-all on already processed FS data ( e.g. recon-all -s ${SUBJECTS_DIR}/$session -hippocampal-subfields-T1 -parallel -openmp 6 -bigventricles -3T -time), I encountered an error. I have attached the log for your viewing. Thank you.

Best,

Miracle