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_tibWCFgxRVp5qMyNCdaPDbahbXesxHSWfDY3t8wvp6OTfje04KDpgHFGDdkoecJv07GtKeuldJJNVJnsuffSVx9LfYzLYeh-1a5ScJN1PdZ-fDNE--Lnv1R4phboTjurWMX43qna0wem5Wa2vhWvLXwEfcGTxqY7Bduq1xk_MKqmJ0BaQptL5lOK-V0kBUTl58fCB2eRrlvBQMoLDzBscjG_cnGqeT3ZMyhoh1X1rv5D7bkil9-4mWA/https%3A%2F%2Fwww.virtualbox.org%2Fmanual%2FUserManual.html%23sharedfolders 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 <[email protected]> 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 > > > > > > > > > _______________________________________________ > Freesurfer mailing > [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1-4gugTG7IJfnMSP9Kbd3NVtUKTt23hOeCLRtobg_9eugEF5QbPwyeJBMkyKRnUEycElhjwY_qKW8n3EOxMBUrO7rwxeCUSjp4j1qOzAxzrKpPV_RJTy1RSNxyqGUyCewq1f9iCpdF2RClubdfNt5C8jGFXfJPOAmLmiZk-4b-CGRZBCXllH9J5SMAGVEGteqtX-K_CxOOiuBZk0raFZN1xAeJl0qAqY_cFG8zTNfCs5wJBUhpuinkEL7eIZOHQhRGdZYRNiHtONcaVRD7crYlw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The 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 > http://secure-web.cisco.com/1MwgiO-I6rZmEaKP4aOBZdZ_lN3KTEvoI5tOu9SKhlrO_PjSav0ImSZjUWc6isdXJxz5MMet1p4a8vqcQSc8z7DNyPQ9UzO9tbZGawhyD4z2sdXaANthxnEH6C-Kd01XWSFmsfeNIgCkjPPrtHfQf2ldNJkcsc_68a560U4p8HW1kXnLcJK2-s-u9zKfCWu3nSu5n-OgnfnFfebyUOPY5fVUXpDRtbqxouQQv6phML8b3x6XMUqqMke9gyroDbRTWUdSbcH0NEosH9DEpE1Oj8Q/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . 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 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: [email protected]
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