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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis
<alandarkene...@gmail.com>
Sent: Friday, August 12, 2022 12:33 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula - Preproc
External Email - Use Caution
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....@gmail.com<mailto:kingwai....@gmail.com>> wrote:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula - Preproc
Yes that's from FSL. It's needs to be in $FSLDIR.
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Alan Francis
<alandarkene...@gmail.com<mailto:alandarkene...@gmail.com>>
Sent: Thursday, August 11, 2022 3:30 PM
To: Freesurfer
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula - Preproc
External Email - Use Caution
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.
_______________________________________________
Freesurfer mailing list
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