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_AR2rQlI8PlEU1VIVMmtW4AXXraRYQrh4EesIh-2zxLL95RZ4uADb94HhLf6bwC4HStrmNBxTN1P6onMGfuO2S4W4uvvwfGIBNqjQiVAZPmx6apNd4RkD__6429s9Dec_A80QMbmZ5p1jH5eSbN_Yy8sjxqJeDxkuw6X14AqP-wtxc7-bvAz65_QiVsYkX5NYR7HCd7X9LJ_qmhN6nk5ccXH_x6XDx5euZhGR99v6Dj/https%3A%2F%2Fstackoverflow.com%2Fquestions%2F56343002%2Fis-it-possible-to-use-symbolic-links-in-virtualbox-shared-folder-without-adminis - R.
On Aug 5, 2021, at 10:20, Kiyotaka Nemoto <kiyot...@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-M2UeXKZtomyLdGKz2hQxzBRgbN5ye_n05Zfy6i5YNSm-x-25yEjp6h819_yq-6XkkGYt7FEZuwuuolHCQWTR-sqNub0Pf4T8SZ5ech1a-XOt0R2j7pKbYcP2AiDn1AZEeiN-1FzCbzAd1OPrZdpQWmDKTLuEUcQI_l28duTwPlf-3v0aiOLOQGoQ_n2r2o86c1tP5E7kGLa3LF4bPG/https%3A%2F%2Fwww.virtualbox.org%2Fmanual%2FUserManual.html%23sharedfoldersI 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 <dgr...@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/1qXkHhWjbbX7kqhyJvxsVIR9MtQArotd4VbtHCKRYOGOQ0LLjWcVVnR46t4fvIWWGcFvSobYPXs-4Ssw2ciHlGXSJvEQtz25xwOnEjg3YZI5burGFvnuo_DEnlH2FHGEXWVf5d55-WEnFz5PMMrE84oUnZwNqfOnw0xQfyq6bBJm6YX_7YKnB3kt6Pg8OWKEVEkgsEqIQGwjtlMuN7RZ7sRCbRYYXRk9Xxp-1W2OFhl3b4QkJhBCjSlbvY992TbU2/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing listfreesur...@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_rgOJnRtQnqFDe1XOdS2eNb64q9B53FQku5EjESybzvgxx0LXKF9uHBO5zwFvd1EebEKmeqdWrtwaUenm6DrpyrP3lFjys3dkRFQyYNt_O-6ZJa7PXeqEks9-dBOxA4lTJQUZ0QcUTHlkKMffDn0zQh6VPZupZcWm6s1k0Mz8rVr72izrYB11UUOZYtMfDN-YGyswQsrW9xSFTZhY_34xfo29hzuPD4ym8t_qNMZf/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2FfreesurferThe 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-Lt1Ak49HgxqWhsfxXQaojr3euAK6ayeMXaijdmbX9kLWZG3N0iwUof2KonQlRkcOoFVcZ-Vx5TuwDhhM8qiDKgAZm22H0mIBI7OaMwNtO2oJaaKUh2YVMjpMydKkSL3jfZkpZBKmfp9TXNtFRdkBzXNXchT2mzMcb4wtHdks3yB5qnlwLUN1cVXeffZih2d9Tuw5EOXZzI-LHq8_vO1zNzaM/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26nbsp;. 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 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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