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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:
External Email - Use CautionHi 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:
External Email - Use CautionHi 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
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 PhDAssistant Professor of NeuroscienceInstitute of Neuroscience*
*University of Texas, School of Medicine*
*Rio Grande Valley*
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*Rio Grande Valley*
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