If you want to use ANTs for registration, you have to have ANTs installed and
set ANTSPATH to its location.
________________________________
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 4:35 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula - Preproc
External Email - Use Caution
Hi Anastasia and King_Wei :
Thank you for your suggestions. I have fixed the bet issue by reinstalling FSL.
But I have one more error:
ERROR: must set ANTSPATH environment variable to use ANTs
I tried setting
set ANTSPATH = 0 but that did not work.
I looked up the web to see if there were any default values I could use for
ANTs but did not come up with any.
Thanks again for your help,
Alan
On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu
<kingwai....@gmail.com<mailto:kingwai....@gmail.com>> wrote:
External Email - Use Caution
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
<alandarkene...@gmail.com<mailto:alandarkene...@gmail.com>> wrote:
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.
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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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--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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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