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Hi Alan,

If you really have FSL installed inside Freesurfer, it is not the way to do it.

If you type

echo $FSLDIR

does it return anything?

If FSL is installed the way you said it is, echo $FSLDIR should give something like

/usr/local/freesurfer/7.2.0-1/FSL

in your system

Also, if you type

which bet

It should return something like

/usr/local/freesurfer/7.2.0-1/FSL/bin/bet

or type

ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet

Does it say "No such file or directory" or return

/usr/local/freesurfer/7.2.0-1/FSL/bin/bet

If you don't get all these, your FSL is not installed correctly.

Best,

King-Wai

On Fri, Aug 12, 2022 at 12:34 PM Alan Francis <alandarkenergy@gmail.com> wrote:

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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

--

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

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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--

King-Wai Chu, Ph.D.
Program Analyst
Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
130 W. Kingsbridge Road
Bronx, NY 10468

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