Can you post the contents of your ~/.bash_profile

On 01/25/2013 01:41 PM, Rosalia Dacosta Aguayo wrote:

Dear Free Surfer experts,

Sorry for posting this again...but I have been trying this all the day and nothing seems to change the situation.

I am having problems with my FS installation. I am working with Linux/Ubuntu version 11.10...I have followed the indications of the FS wiki and it seems that it is installed but it does not work...it does not run in the terminal and I do not know why and how can I do:

osi@rosi-HP-Pavilion-dv9700-Notebook-PC:~$ cd /home/rosi/FREE_SURFER/ freesurferrosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ export FREESURFER_HOME=/home/rosi/FREE_SURFER/freesurfer rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ . $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos4-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/rosi/FREE_SURFER/freesurfer FSFAST_HOME /home/rosi/FREE_SURFER/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/rosi/FREE_SURFER/freesurfer/subjects MNI_DIR /home/rosi/FREE_SURFER/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ freesurfer

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer also refers to the structural imaging stream within the FreeSurfer suite.

Users should consult the online documentation available at:

https://surfer.nmr.mgh.harvard.edu https://surfer.nmr.mgh.harvard.edu/

Alternatively, the 'recon-all' command help-text provides adequate information to begin processing subject data, such as the sample subject 'bert' found in the 'freesurfer/subjects' directory. Type 'recon-all --help' to view this help-text.

Direct comments and questions to:

freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu

*You are running this version of FreeSurfer:

freesurfer-Linux-centos4-**stable-pub-v5.1.0

rosi@rosi-HP-Pavilion-dv9700-* *Notebook-PC:~/FREE_SURFER/**freesurfer$

How can I call FreeSurfer??

*Thanks in advance,

Rosalia.

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