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:
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
<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:
* 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
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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