Hello Stefano,

It looks like you do not have permission to write to /usr/local/freesurfer/subjects/bert

If multiple people will be using the data there at the same time, then it is probably not a good idea for everyone not to be writing to the same location.

An alternative is to set the environment variable SUBJECTS_DIR to point to a copy of the ./bert subdirectory under a path you can both read from and write to.

I think the ./bert subdir is about 400M, so you could try copying it somewhere, e.g., to your $HOME directory. So if you ended up with $HOME/bert as the path to the data, then you would set SUBJECTS_DIR to $HOME in your shell.

- rob

On May 9, 2018, at 1:20 PM, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:

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This errors are occurring when we test FreeSurfer Installation on our server:

1) ubuntu01:/usr/local/freesurfer/subjects> mri_convert sample-001.mgz sample-001.nii.gz mri_convert.bin sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... niiWrite(): error opening file sample-001.nii.gz ERROR: failure writing sample-001.nii.gz

2) ubuntu01:/usr/local/freesurfer/subjects> recon-all -i sample-001.nii.gz -s bert -all mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/bert/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-stable-pub-v6.0.0-2beb96c /usr/local/freesurfer/subjects/bert/scripts/patchdir.txt: No such file or directory.

3) ubuntu01:/usr/local/freesurfer/subjects> freeview -v sample-001.mgz freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory

Thanks

Stefano

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