I have explicitly set it like Nick suggested and ensured I have also sourced FreeSurferEnv.csh. Same result unfortunately.

On Tue, Nov 18, 2008 at 5:08 PM, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote:
Christian,

You may want to try explicitly setting your freesurfer home prior to
sourcing, like this:

setenv FREESURFER_HOME /home/user/Desktop/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

i noticed in your output it has the path as 'Desktop/freesurfer', which
is not a full path, and probably that is why it is not finding the
commands.

Nick


On Tue, 2008-11-18 at 16:04 +0000, Christian Lambert wrote:
> I'm just starting out with freesurfer. I am using CentOS5 Linux shell
> on a windows machine using Freesurfer V4.1.0 with the monitor settings
> on 32bit. I have set up the license file and also configured
> freesurfer as per the wiki pages:
>
> [user@localhost ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.csh
> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   Desktop/freesurfer
> FSFAST_HOME       Desktop/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii
> SUBJECTS_DIR      Desktop/freesurfer/subjects
> MNI_DIR           Desktop/freesurfer/mni
>
>
> Now when I  run recon all (using my own data) I get the following
> error message:
>
> Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0
> Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0
> INFO: SUBJECTS_DIR is /home/user/Desktop/freesurfer/subjects
> Actual FREESURFER_HOME /home/user/Desktop/freesurfer
> Linux localhost.localdomain 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24
> 19:33:52 EDT 2008 i686 athlon i386 GNU/Linux
> mri_motion_correct.fsl: Command not found.
> flirt: Command not found.
> talairach_avi: Command not found.
> tkregister2_cmdl: Command not found.
> nu_correct: Command not found.
> mri_normalize: Command not found.
> ....
> ...
> ....
> mris_make_surfaces: Command not found.
> mris_register: Command not found.
> mris_anatomical_stats: Command not found.
> mrisp_paint: Command not found.
> cp: cannot stat `Desktop/freesurfer/bin/recon-all': No such file or
> directory
> /home/user/Desktop/freesurfer/subjects/chris2
>
> mri_watershed: Command not found.
>
>
> I have been through the manual, wiki pages and seached the mailing
> list extensively but could not find a solution to this problem. I
> notice one similar thread in 2006 but it never detailed how the
> problem was solved, but based on that I include the line below:
>
> [user@localhost ~]$ ldd 'which mri_convert'
> ldd: ./which mri_convert: No such file or directory
>
> Thanks for any insight you can provide.
>
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