Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

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Hi Anastasia,

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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).

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Thanks,

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King-Wai

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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

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

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Anastasia.

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

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Hi Douglas,

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Thank you for looking into this.

It gives the following error.

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trac-preproc.sh -c config.file

intrareg: Undefined variable.

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Thanks,

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King-Wai

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From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto: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 mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

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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 mailto:kingwai.chu@gmail.com wrote:

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Hi Anastasia,

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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

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trac-all finished w/o problem.

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trac-all -version

trac-all 7.3.0

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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?

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Is my fix correct?

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Thanks,

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King-Wai

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