External Email - Use Caution

If you are running Virtualbox to host linux on a windows machine sharing a folder from a windows NTFS file system, then it may not work to create soft links in linux on the mounted share w/o setting some things on the Windows side.  I’m not up on what current versions of VirtualBox support for creating soft links in a linux file system on top of the (different) NTFS file system, but here is some info from ~2 years ago, https://secure-web.cisco.com/1FAdsc9WBYl3JetwHMp2nc_AR2rQlI8PlEU1VIVMmtW4AXX... - R.

On Aug 5, 2021, at 10:20, Kiyotaka Nemoto <kiyotaka@nemotos.net> wrote:        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: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1SzkQ16diCzjzLRbWT9fZxbUN_qVihhNUAbkqhDWMHpIn3-... 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/binsudo cp recon-all recon-all.origsudo sed -i 's/ln -s $hemi/cp $hemi/' recon-allsudo sed -i 's/ln -s $FREESURFER_HOME/subjects/fsaverage/cp -r $FREESURFER_HOME/subjects/fsaverage $SUBJECTS_DIR/' recon-allsudo 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,KiyotakaOn Thu, Aug 5, 2021 at 10:42 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:Look in /media/sf_T1/recon/demo3/surfDoes lh.white.preaparc.H exist?If so, does lh.white.H exist?If not, what happens when you runln -s lh.white.preaparc.H lh.white.Hin 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..0-2beb96c2) 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/Linux4) recon-all.log: see attached5) batch .sh file:see attachedThank you  for any reply.zhaoguang  _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1qXkHhWjbbX7kqhyJvxsVIR9MtQArotd4VbtHCKRYOGOQ0L... mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1II6DOs_uxItsRQUh3upLmjq_rgOJnRtQnqFDe1XOdS2eNb... information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/16Inw7HJ6kpX4IG1P-lnhb3mwA7tevjm5pPEH7e6-Lt1Ak49...;. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. --Kiyotaka Nemoto, M.D., Ph.D.Associate ProfessorDepartment of PsychiatryDivision of Clinical Medicine, Faculty of MedicineUniversity of Tsukuba1-1-1 Tennodai Tsukuba, Ibaraki 305-8575, JapanE-mail: kiyotaka@nemotos.net_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer