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Hi Anastasia and King wei -

I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL is part of that installation. Do you recommend a second installation of FSL separately?

Thanks so much for your help and comments!

Alan

On Thu, Aug 11, 2022 at 2:50 PM <kingwai.chu@gmail.com> wrote:

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Hi Alan,

 

As Anastasia said, bet is part of FSL.

If you don’t have it installed already, you need to install FSL.

 

Best,

 

King-Wai

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yendiki, Anastasia
Sent: Thursday, August 11, 2022 3:42 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula - Preproc

 

Yes that's from FSL. It's needs to be in $FSLDIR.

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis <alandarkenergy@gmail.com>
Sent: Thursday, August 11, 2022 3:30 PM
To: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Tracula - Preproc

 

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Hi Anastasia, King Wei:

 

I did as you suggested with the config file and the preprocessing ran for a bit but then an error occurred. I have attached the run script. It says BET not found. Is this the Brain Extraction tool?

 

Could you please shed some light on this?

 

thanks so much,

 

Alan

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|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience

University of Texas, School of Medicine

Rio Grande Valley

Texas.

                                                                                                          

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Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience

University of Texas, School of Medicine

Rio Grande Valley

Texas.

                                                                                                          

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