Re: [Freesurfer] recon-all mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied error
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Hello Rana, Looks like you are missing a capital S at the end of SUBJECT or it’s SUBJECTS_DIR instead of SUBJECT_DIR. $ export SUBJECTS_DIR=/home/banikr2/273_p So the default SUBJECTS_DIR, /usr/local/freesurfer/subjects, ended up getting used, and you do not have permission to write there.
- 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/freesurferI 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_64-7.1.1-20200723-8b40551I 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/1gXITlegvJK1p_-l14FbolcoT9opnCLyCP3dD_NY... I performed accordingly. Any suggestions?Rana Banik_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OG3BAo0lmU7cE8cn9LvmHGOEYJzbtbgtwdIvUeIwpOy9kX...
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Hello, Thanks. I think I am missing .license file somehow:
banikr2@banikr:~$ export SUBJECTS_DIR=/home/banikr2/273_p banikr2@banikr:~$ recon-all -s sub273 -i 273_p/273_MR.nii Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /home/banikr2/273_p Actual FREESURFER_HOME /usr/local/freesurfer Linux banikr 5.4.0-80-generic #90~18.04.1-Ubuntu SMP Tue Jul 13 19:40:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/home/banikr2/273_p/sub273/scripts/recon-all.local-copy' /home/banikr2/273_p/sub273
mri_convert /home/banikr2/273_p/273_MR.nii /home/banikr2/273_p/sub273/mri/orig/001.mgz
mri_convert /home/banikr2/273_p/273_MR.nii /home/banikr2/273_p/sub273/mri/orig/001.mgz -------------------------------------------------------------------------- ERROR: FreeSurfer license file /usr/local/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://secure-web.cisco.com/1GzvHSb251Yr6P5cfHy6esfJq6ZSKmJfdQy6sBL_o8C2BiZK... to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. A path to an alternative license file can also be specified with the FS_LICENSE environmental variable. -------------------------------------------------------------------------- reading from /home/banikr2/273_p/273_MR.nii... Command exited with non-zero status 255 @#@FSTIME 2021:09:26:18:57:22 mri_convert N 2 e 0.00 S 0.00 U 0.00 P 100% M 6312 F 0 R 243 W 0 c 0 w 1 I 0 O 0 L 0.37 0.32 0.27 @#@FSLOADPOST 2021:09:26:18:57:22 mri_convert N 2 0.37 0.32 0.27 Linux banikr 5.4.0-80-generic #90~18.04.1-Ubuntu SMP Tue Jul 13 19:40:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub273 exited with ERRORS at Sun Sep 26 18:57:22 CDT 2021
For more details, see the log file /home/banikr2/273_p/sub273/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1soqVSUvnV4acp-IDY-p0cePPm3tNohXKMIkVASKxyzL3BKl...
Downloaded license.txt file and moved it to /usr/local/freesurfer:
banikr2@banikr:~$ sudo cp Downloads/license.txt /usr/local/freesurfer/license.txt
banikr2@banikr:~$ recon-all -s sub273 -i 273_p/273_MR.nii ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags.
Rana Banik
________________________________ From: fsbuild fsbuild@contbay.com Sent: Sunday, September 26, 2021 3:45 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
Hello Rana,
Looks like you are missing a capital S at the end of SUBJECT or it’s SUBJECTS_DIR instead of SUBJECT_DIR.
$ export SUBJECTS_DIR=/home/banikr2/273_p
So the default SUBJECTS_DIR, /usr/local/freesurfer/subjects, ended up getting used, and you do not have permission to write there.
- 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/1xyEw-Du7VDw6UQMDOBvoXPa5poULux7AgHcYv-Z...https://secure-web.cisco.com/1UyRerrfXnNJVXBgNnjOaGNCffXW42SxgzKzVozNe5equ7FSLsqGXNKqNFdVrCkTcF1rkDb1ozLDpnydlvZu9lasNb3k8K8-JEjKmw0RATB_g_v7j9tz2W_gWS4P95gYkdhc1vEPou7B-rBgPujmHpdqlcO3NFmcRzgrc8v6CIhJ5uv2F0RcuguSJu7nQ3iTcIZ3tAmUf0SeH95QjDiYK9kaBAUaVQ3t1HgZdh4GtXkNCX49DNSZRFKjjG0SbY54B8sEz24kav1qzX68-ltFiOw/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%257C221e16e6a9024d8337d608d9812ea2c0%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C637682859582635744%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3Dx%252FUlsPVM6n%252Bc41mqiezxndZBVTdhc8yjRKii2kv7Q2M%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/1t1OnJ_56gfxSWzbSJmbM2iJMXkwoKWz9Wtu8Iu88AqTXTT2yoxX8CCpp-Gsx_G35p7tWV1QWwAWNIbkgatAO1WRyyc9Ay53d3ESIOOEAgCTynWp8BwmH2N_CHSbwzC85KAJV_zyrJnkf7I790AIdVBhceq_cy4__vQqgzkuXhKhy_41VaK50sjW2QL-fXs4nraiSvWqRqdF836aEkrnPIft5dLbgezGt43qnKWOjlnlq0R7RiH8szS1LtEWccGAF4bvmPrLJQpaUWncTXojjmw/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%257C221e16e6a9024d8337d608d9812ea2c0%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C637682859582645737%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DVtfqjhxwnyCSe3LU1S9rq63AzlvXpiU1e46NnTKZz%252FE%253D%26reserved%3D0
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