External Email - Use Caution

Hi,

I think the problem is caused because Zhaoguang uses a VirtualBox share folder. The path "/media/sf_T1/" indicates the path is a shared folder of VirtualBox.

Symbolic links can be used on some certain conditions. Source: https://secure-web.cisco.com/1dwlgJDipuhkA56EdBKvdgjX7GQ06QB_tibWCFgxRVp5qMy...

I think there are two workaround options.

1. Avoid using shared folders If you copy your T1 image from shared folder to somewhere on your Linux guest, recon-all should go well.

2. Change "ln -s" to "cp" in recon-all I tweak recon-all a little bit so that recon-all works well with files on VirtualBox shared folders. The commands below makes backup of recon-all first, then substitute "ln -s" with "cp" or "cp -r"

===== cd $FREESURFER_HOME/bin sudo cp recon-all recon-all.orig

sudo sed -i 's/ln -s $hemi/cp $hemi/' recon-all sudo sed -i 's/ln -s $FREESURFER_HOME/subjects/fsaverage/cp -r $FREESURFER_HOME/subjects/fsaverage $SUBJECTS_DIR/' recon-all sudo sed -i 's/ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average/cp -r $FREESURFER_HOME/subjects/${hemi}.EC_average $SUBJECTS_DIR/' recon-all =====

Hope this helps,

Kiyotaka

On Thu, Aug 5, 2021 at 10:42 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

Look in /media/sf_T1/recon/demo3/surf Does lh.white.preaparc.H exist? If so, does lh.white.H exist? If not, what happens when you run ln -s lh.white.preaparc.H lh.white.H in that folder?

On 8/5/2021 1:41 AM, guang wrote:

    External Email - Use Caution

Hello FreeSurfer Developers, I'm attempting to preprocess my nii.gz files with FreeSurfer, But some errors occurred when I recon-all the data. I've attached the batch script and recon-all.log in case it's of any use.

1. FreeSurfer version:

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: CentOS release 6.10 (Final) 3) uname -a: Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached 5) batch .sh file:see attached

Thank you for any reply.

zhaoguang

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-- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1 Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyotaka@nemotos.net