Hi Heidi

can you give us the full screen output and exact command you are running? And what shell are you using? In csh/tcsh you can have an env variable be superseded with a set command. For example:

setenv SUBJECTS_DIR right set SUBJECTS_DIR=wrong

will cause getenv to get wrong. Also, try specifying it explicitly on the recon-all command line to avoid any of this type of problem

cheers Bruce

On Sun, 29 Apr 2018, Jacobs, H (NP) wrote:

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Dear FreeSurfer,

I just installed FreeSurfer6 on my computer and tried to run a subject (license file is set). I sourced freesurfer and have set the subjects_dir. However, when running the recon-all, I get the following error :

ERROR: cannot find /Applications/freesurferv6/subjects/S006

And running echo $SUBJECT_DIR gives me this output:

/Users/heidi/Desktop/tryout

Any suggestions what may be the problem?

Thank you Heidi