Yes, my original config file works with 7.2

I really appreciate your help.

Thanks.

King-Wai

I don't know; Anastasia is the author. She's busy today and tomorrow, I was just trying to push it forward. Does it work with the given config file in 7.2?

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I added it to the config file, then it complains

interreg: Undefined variable.

 

When I added interreg = 5, then it complains

subj: Undefined variable.

 

Should I continue fixing it until no more Undefined variable?

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 5:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 

I think the wiki is wrong. Try setting it to 3 in the config

On 7/25/2022 5:30 PM, kingwai.chu@gmail.com wrote:

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Hi Douglas,

 

According to

TRACULA tutorial

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A very simple configuration file, where only the absolutely necessary inputs are specified, intrareg is not there.

and it works on v7.2.0. w/o it explicitly specified.

 

From the same site above,

Step 12: Specify the intra-subject registration method

“The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT with a mutual information cost), and 3 (bbregister, which uses a boundary-based cost). The default is option 3 (bbregister).”

 

If I don’t specify it in the config file, it should automatically use the default setting which is intrareg = 3.

 

I will add it to the config file and try again.

 

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 5:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 

are you sure the config file is right? it should be defining the intrareg variable

On 7/25/2022 2:11 PM, kingwai.chu@gmail.com wrote:

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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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