Thanks so much for the speedy response,

Using the export command you recommended didn't give me any problems.

However, I've downloaded the new version, but when following the steps for set up the terminal is still trying to use the old fsfast file path:


[vbecker@bhfilbey ~]$ export FREESURFER_HOME=/home/vbecker/freesurferV6
[vbecker@bhfilbey ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
WARNING: /home/jdunlop/freesurfer/subjects does not exist
FREESURFER_HOME   /home/vbecker/freesurferV6
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR      /home/jdunlop/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
FSL_DIR           /usr/local/fsl


Is there a way to change this to my user file path permanently? Or will I need to manually correct the SUBJECTS_DIR with the export command every time?


Thanks,

Valerie

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Z K <zkaufman@nmr.mgh.harvard.edu>
Sent: Tuesday, May 23, 2017 2:37:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Problems changing automatic SUBJECTS_DIR file path
 
Hi Valerie,

It looks like you might be using bash shell, in which case you should be
using the 'export' command instead of setenv to change its value (note
the difference in syntax):

   export SUBJECTS_DIR=<full path to subject dir>

Please note... It looks like you are using a very old version of
freesurfer. Freesurfer 4.5 was released well over 5 years ago.


On 05/23/2017 03:31 PM, Becker, Valerie wrote:
> Hi FreeSurfer Developers,
>
>
> I'm new to Linux as well as freesurfer and picking up with the program
> where an old lab assistant left off. He already installed the program
> and fsfast, but set the subjects directory using a file path unique to
> his user and I'm having trouble changing it. Calling up the terminal
> gives me this output automatically:
>
>
> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> WARNING: /home/jdunlop/freesurfer/subjects does not exist
> FREESURFER_HOME   /usr/local/freesurfer
> FSFAST_HOME       /usr/local/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii
> SUBJECTS_DIR      /home/jdunlop/freesurfer/subjects
> MNI_DIR           /usr/local/freesurfer/mni
> FSL_DIR           /usr/local/fsl
>
>
> I've been unable, thus far, to find a way to change file path the
> SUBJECTS_DIR is using and trying the setenv command from the website
>
>
> setenv SUBJECTS_DIR <full path to subject dir>
>
>
> with the correct file path input, the terminal output gives me:
>
>
> [vbecker@bhfilbey ~]$ setenv SUBJECTS_DIR /home/vbecker/freesurfer/subjects
> bash: setenv: command not found
>
>
> I also wasn't able to find a direct reference to this issue searching
> the archives. Any help would be much appreciated.
>
>
> FreeSurfer Version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0
>
> Platform: CentOS Release 6.9 (Final), Kernel Linux
> 2.6.32-573.7.1.el6.x86_64, GNOME 2.28.2
>
>
> Thanks,
>
> Valerie
>
>
>
>
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