Good to hear, thanks for testing it. We'll implement a permanent solution so you won't have to replace anything in the future.

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com <kingwai.chu@gmail.com>
Sent: Monday, August 1, 2022 12:44 AM
To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 

        External Email - Use Caution        

Hi Anastasia,

 

I thought he wants me to run trac-preproc.sh he sent to run it directly.

I wasn’t told to replace it with the one in the original 7.3.

 

After replacing the original one with the modified one Doug sent, trac-all -prep -c config.file runs w/o problem.

 

Thanks,

 

King-Wai

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:15 AM
To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 

Indeed. Doug sent you a modified version of trac-preproc, which is a script that's called by trac-all. The idea was for you to overwrite $FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run trac-all like before. Did you try that?

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com <kingwai.chu@gmail.com>
Sent: Monday, August 1, 2022 12:10 AM
To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 

        External Email - Use Caution        

Hi Anastasia,

 

The problem is in 7.3, trac-all -prep -c config.file is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

 

Thanks,

 

King-Wai

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:03 AM
To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 

Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile, like before.

 

Anastasia.

 

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of kingwai.chu@gmail.com <kingwai.chu@gmail.com>
Sent: Monday, July 25, 2022 2:11 PM
To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 

        External Email - Use Caution        

Hi Douglas,

 

Thank you for looking into this.

It gives the following error.

 

trac-preproc.sh -c config.file

intrareg: Undefined variable.

 

Thanks,

 

King-Wai

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 

Can you copy the attached trac-preproc into $FREESURFER/bin and try again (after removing the link)?

On 7/22/2022 8:36 AM, kingwai.chu@gmail.com wrote:

        External Email - Use Caution        

Hi Anastasia,

 

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ThalamicNuclei.v12.T1.FSvoxelSpace.mgz

 

trac-all finished w/o problem.

 

trac-all -version

trac-all 7.3.0

 

I seems trac-all in v7.3 forgets to update the fact that segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?

 

Is my fix correct?

 

Thanks,

 

King-Wai

 

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