Hi Neda,

That’s unusual - can you send the output of sourcing the file in a debug shell:

sh -x

export FREESURFER_HOME=/usr/local/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.sh

You’ll probably have to ctrl-c to stop this as well. After running it, can you also send the ouput of:

env | sort

thanks,

Andrew

From: Neda Mohammadi <n55mohamadi@gmail.com>
Date: Sunday, March 11, 2018 at 6:30 AM
To: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Cc: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Installation problem

Hi Andrew,

Thanks for your reply. It repeat the freesurfer startup message .

-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Work/Processed_data/freesurfer
MNI_DIR           /usr/local/freesurfer/mni
FSL_DIR           /usr/share/fsl/5.0
Best regards

On Wed, Mar 7, 2018 at 11:56 PM, Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:

Hi Neda,

What’s going on exactly? Is the source command hanging or is it repeatedly printing the freesurfer startup message?

best

Andrew

On March 7, 2018 at 3:03:38 AM, Neda Mohammadi (n55mohamadi@gmail.com) wrote:

Dear Expert,

I tried to install Freesurfer on Ubuntu 16.0.4. I've followed these steps:

1. Download and extract into the directory /usr/local
2.export FREESURFER_HOME=/usr/local/freesurfer

Its fine, but when I run this step

3.source $FREESURFER_HOME/SetUpFreeSurfer.sh

I receive this message n time

-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Work/Processed_data/freesurfer
MNI_DIR           /usr/local/freesurfer/mni
FSL_DIR           /usr/share/fsl/5.0

and I must press Ctrl+C to stop.
What do I do now?

--

Best Regards,

Neda

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Best Regards,

Neda