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: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.virtualbox.org/manual/UserManual.html#sharedfolders

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