Earlier versions of TRACULA didn't have the option to use ANTs for registration. Now you have that option, but you also have the option not to use it, if you're finding it hard to install.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis <alandarkenergy@gmail.com>
Sent: Wednesday, August 17, 2022 4:46 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula - Preproc
 

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Thank you King Wai and Philip. I am reworking the config file to see if that works. The earlier Tracula versions were much easier to run.

best,

Alan

On Mon, Aug 15, 2022 at 3:15 PM King-Wai Chu <kingwai.chu@gmail.com> wrote:

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Hi Alan,

Check the ANTs version. If you are using the binaries version  2.1.0
"antsRegistration --version" should return
All_Command_lines_OK
ANTs Version: 2.1.0-g78931
Compiled: Jan 23 2015 03:27:59

If not, you are not using the version 2.1.0

Do you know where is the binaries?
You need to change ANTSPATH to point to the binaries.

Or open a new terminal and try again.

Best,

King-Wai



On Mon, Aug 15, 2022 at 3:46 PM Alan Francis <alandarkenergy@gmail.com> wrote:

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Hi King Wai -

Thanks for your help. I downloaded version 2.1.0 as you suggested and installed it. But the error message keeps coming back. It is looking for this file:

/home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh

But this file is not present in the binary folder.

Thanks,

Alan

On Mon, Aug 15, 2022 at 12:54 PM King-Wai Chu <kingwai.chu@gmail.com> wrote:

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Hi Alan,

First find out the version of ANTs you have by running the command below
antsRegistration --version

If it is below 2.1.0
download the 2.1.0 binaries here, it works for me.

If you want to use your script, edit the yellow lines to remove "#"
# If you want to build a particular release, do so here
# cd ANTs
# git checkout v2.3.1
# cd -

# If you want to build a particular release, do so here
cd ANTs
git checkout v2.3.1
cd -

you can also try v2.3.5 or v2.4.0.

I don't know if it will work or not because I don't write this script.

Best,

King-Wai

On Mon, Aug 15, 2022 at 1:15 PM Alan Francis <alandarkenergy@gmail.com> wrote:

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Hi King Wai -

I used a script (enclosed) to install ANTs. Is there anyway this script could be modified to install the latest version?

Thank you so much,

Alan

On Mon, Aug 15, 2022 at 11:40 AM King-Wai Chu <kingwai.chu@gmail.com> wrote:

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Hi Alan,

Do you have the latest version of ANTs?
It should be 2.1.0
Older version don't have all the binaries and scripts required by trac-all.

Best,

King-Wai

On Mon, Aug 15, 2022 at 11:49 AM Alan Francis <alandarkenergy@gmail.com> wrote:

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Hello King Wai -

I used the C shell pathway just as you specified. But I got this error message right at the end of the processing:

#@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022
/home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m /home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f /usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o /home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn
/home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not found.
Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT 2022 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022

In the installed ANTs folder I could not find the antsRegistrationSyNQuick.sh script. Should I create this script?

Thanks ever so much!

Alan

On Mon, Aug 15, 2022 at 10:13 AM Alan Francis <alandarkenergy@gmail.com> wrote:
Thank you so much King Wai,

On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu <kingwai.chu@gmail.com> wrote:

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For bash shell
ANTSPATH=/home/afrancis/Imaging/ANTs

For tcsh
setenv ANTSPATH /home/afrancis/Imaging/ANTs

On Fri, Aug 12, 2022 at 5:54 PM Alan Francis <alandarkenergy@gmail.com> wrote:

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Hi Anastasia :

I installed ANTS and tried this

set ANTSPATH = /home/afrancis/Imaging/ANTs

but it did not work. Is there a different set path?

Thanks,

Alan

On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:
If you want to use ANTs for registration, you have to have ANTs installed and set ANTSPATH to its location.
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 4:35 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula - Preproc
 

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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.chu@gmail.com> wrote:

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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


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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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--
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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.
                                                                                                          


--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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
_______________________________________________
Freesurfer mailing list
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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
_______________________________________________
Freesurfer mailing list
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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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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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.