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.edumailto: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.commailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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-- Best Regards, Neda