ent:* Monday, August 1, 2022 12:44 AM
> *To:* 'Freesurfer support list'
> *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
Cc: kingwai@gmail.com
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution
There is a change related to that,
Date: Mon Jul 25 21:24:30 2022 -0400
trac-preproc. #BF. Changed expected thalseg version to 1.3; also added an
option to be able
External Email - Use Caution
There is a change related to that,
Date: Mon Jul 25 21:24:30 2022 -0400
trac-preproc. #BF. Changed expected thalseg version to 1.3;
also added an option to be able to spec the thalseg file. AY should look at it.
- in the latest development builds,
support list'
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
config.file runs w/o problem.
�
Thanks,
�
King-Wai
�
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:15 AM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
Indeed. Doug sent you a modified
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of kingwai@gmail.com
Sent: Monday, August 1, 2022 12:10 AM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution
Hi Anastasia,
The problem is in 7.3, trac-all -prep
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).
�
Thanks,
�
King-Wai
�
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:03 AM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
Hi King-Wai
list'
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-boun
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
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?
On 7/25/2022 5:46 PM, kingwai@gmail.com <mailto:king
*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@gmail.com wrote:
*External Email - Use Caution *
Hi Douglas,
According to
TRACULA
...@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@gmail.com
.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
�
�
�
�
�
From: freesurfer-boun...@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
: Undefined variable.
Thanks,
King-Wai
*From:*freesurfer-boun...@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
. 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@gmail.com
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@gmail.com wrote:
External Email - Use Caution
Hi Anastasia,
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all
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
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