The error message that you got says that the bet command isn't in your Unix path. You need to fix that, so that you don't get that error. If bet and all the other FSL executables are already installed somewhere on your computer, you need to add that directory to your Unix path. I'm not sure what "It shows that FSL is part of that installation" means (what does "it" refer to?), but if "which bet" doesn't show you a directory where bet can be found, you won't be able to get any further.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis <alandarkenergy@gmail.com>
Sent: Friday, August 12, 2022 12:33 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula - Preproc
 

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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.