External Email - Use Caution
Thanks -R for helping me troubleshoot. I could run the following with no error.
banikr2@banikr:~$ recon-all -s sub273 -i 273_p/273_MR.nii
I had downloaded and moved the license.txt file in:
/usr/local/freesurfer/
I hope there are no other installation checks or whatsoever. Thanks again.
Rana ________________________________ From: fsbuild fsbuild@contbay.com Sent: Sunday, September 26, 2021 7:32 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Banik, Rana rana.banik@vanderbilt.edu Subject: Re: [Freesurfer] recon-all mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied error
OK - fill out the form on this page and download the license.txt file,
https://secure-web.cisco.com/1JbGB5tVAQj4XQlemOae3xY2Fl8D4DprciD-T368MDehO6T...https://secure-web.cisco.com/17eKxUH-h61tU-_SuYd33v-s-MsHcokCI-jXFC4ZSvR2IpC8YHxHjvZvyRk4JuoQvojzS4oLXxM5AQaKWSafDSQLqaIO5Wq6cA8vyIMucJEhgXYbcwln902y7LzKPhCcuM6SDO9hsIRN4ktZgLVCZE6r2HWORiJvyMizZ1c6gYUCaDVTEKzCx72yDwPZCcVCzss4a1J8sGXHL9cRGrWYH1vn2tNcEP0Q6uo1kp-yscJYTrhz73LxYmGX4NIVVBS_HG04Wi7jHoYnCY0szcl7J8Q/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Fregistration.html%26data%3D04%257C01%257Crana.banik%2540vanderbilt.edu%257C0a7c939c319f41ab295708d9814e4d5c%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C637682995592007180%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DM0KO%252F4sGftnoigsi%252FT0wTaBRlzJG2l4W0Icw8SYshKY%253D%26reserved%3D0
You can copy license.txt to your home directory, e.g., if it’s in your Downloads folder from downloading via the browser,
$ cp $HOME/Downloads/license.txt $HOME/.
Then you can set the environment variable FS_LICENSE to it’s location,
$ export FS_LICENSE=$HOME/license.txt
… check it is readable …
$ cat $FS_LICENSE
You can put the license.txt anywhere just as long as FS_LICENSE is set to point to it.
Then try your commands again.
- R.
On Sep 26, 2021, at 14:10, Banik, Rana rana.banik@vanderbilt.edu wrote:
External Email - Use Caution External Email - Use Caution I installed freesurfer here:
banikr2@banikr:~$ which freesurfer /usr/local/freesurfer/bin/freesurfer
I am getting the following error while running recon-all:
banikr2@banikr:~$ export SUBJECT_DIR=/home/banikr2/273_p banikr2@banikr:~$ recon-all -s sub273 -i 273_p/273_MR.nii mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
I found this from previous troubleshoot emails of freesurfer here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/13mBtUeYFv_YXz9U6irIIrE5c5lV7hg7ZmyRTGHN...https://secure-web.cisco.com/1z4C8PNzMjjzramvClUHqN_nBO78cee0f7YCp9E7fsYOkuEB1uXZHcNgNgrdGgiSCaF85jc1GPRH4wq97s1kvbqI4IDlARtULCIpKCYojuu4JRIJ_4z3-IuHd9jkYBbv7cFTZxND0bfDqMrfJt9mYhqMDn9U07dFrmG_cdvZ-zpc8KdM82UE0Xz4vYhkcaHwAdbH_T9BPKUgtwgNvHOd3kshcZK7u0NxvJzr6HwlsvhE1t6TXJ8Uu09-Irf0ulnZ_oUvUd0k02HBDRPftGF_gkw/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1bocVcL-uht7sTBBGDhGvGZzup63MHVzmcTNCz1auLpZYPeqT1GeMIyavy5XOugapiOkHjHLb3xqBXL1Z_WepYrlJQjdYore5YyJE9q8qLRmPSt_x1AncElEJ6ma0Wi7jsZ4L8Zb6hqNw6DRNBQT8oCXXqZs4bHcZ-xvmBk_6JfWPnY_Drh3KCL9KwEV0mYJOOF0-xSuIoiaFn1W1ChVRkbXu-mMj10R7fJ8F-5zEMw4xqV4F65KbS013zyu2YhkA3nkmB39QmcZSuJ0zzN0mtQ%252Fhttps%25253A%25252F%25252Fwww.mail-archive.com%25252Ffreesurfer%252540nmr.mgh.harvard.edu%25252Fmsg65221.html%26data%3D04%257C01%257Crana.banik%2540vanderbilt.edu%257C0a7c939c319f41ab295708d9814e4d5c%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C637682995592017174%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DpO5ZRxJifHIjGYWz7PYhepqhY6bQc1iIlprWt85bIH0%253D%26reserved%3D0 which I performed accordingly.
Any suggestions?
Rana Banik _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1OG3BAo0lmU7cE8cn9LvmHGOEYJzbtbgtwdIvUeIwpOy9kX...https://secure-web.cisco.com/1Pzt-AFXU3LI5cfompzgRpoaIdmUatHZQ1qTJefRIOj0irlD3gE2d5k5J4fplvZ-nCGSGjN0O-geJdusQIiaWWBydO6fXqR4EHynEILDGB0VQMbwy1SUMy_kNdT9SK0YVyFpfssqYVoy6YU2HZQRcIhJJfTo1c1SrUa2W574MMjnUBVUqH5FCpkKhClH3vtNmhUz6-41RMgRjPLUBYCvVcwL4k_c3hBJeRyrNnBLah9JOrd8MTi1x-ZON1mjiEMQLKMNt-Ec0R8HyxWE-2yhh5g/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1OG3BAo0lmU7cE8cn9LvmHGOEYJzbtbgtwdIvUeIwpOy9kXhVQ-h2j_LveMzWwYTkZ2AqEE8r0GJeWpLjEPOHdUK_hrAe6A9nF9duhTCbe1ACFFJzElxg8IrW7vAtVlSF1RXP7Dr0UUnskPRn4eZT5x9kfwr2t9JxN_OGawnuSTnvIK_SWF89JiymqD7T0csS5MzLGkbeUHy_l-JCJTAYaDIaRkN2AG8adtZhWjjaeeAKbBu14kofu7r8rX6JautSUQCIP5jw9zJhJVfqIlHAOQ%252Fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26data%3D04%257C01%257Crana.banik%2540vanderbilt.edu%257C0a7c939c319f41ab295708d9814e4d5c%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C637682995592017174%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3Dmbdc%252B60a39UOQmgBfxF1oI2rBNyk%252FlX%252BgwEJ3VGbc%252Bw%253D%26reserved%3D0