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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
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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
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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:
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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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