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 wrote:
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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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 wrote:
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Hi Douglas,
According to
TRACULA tutorial
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https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto: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 the
intrareg variable
On 7/25/2022 2:11 PM, kingwai....@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto: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 into $FREESURFER/bin
and try again (after removing the link)?
On 7/22/2022 8:36 AM, kingwai....@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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