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://surfer.nmr.mgh.harvard.edu/registration.html 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://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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.

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

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://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65221.html

which I performed accordingly.

Any suggestions?

Rana Banik

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