External Email - Use Caution
Hi, Lauren Stephens.
If you change some codes in trac-preproc ( in path/freesurfer/bin ), you
can get an aparc+aseg+thalnuc.nii.gz file without error, and make
subthalamic nuclei related tracks.
#chage codes from
set cmd = mri_binarize
set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)
#to
set cmd = mri_convert
set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd -o $labdir/anatorig/${segname}+thalnuc.nii.gz)
Woo-Suk, Tae Ph.D.
Seoul, Korea
On Fri, Oct 6, 2023 at 11:42 PM Lauren Stephens <laure...@stanford.edu>
wrote:
> External Email - Use Caution
>
> Hi FreeSurfers,
>
> I am trying to troubleshoot an error during TRACULA preprocessing and the
> issue seems related to the creation of aparc+aseg+thalnuc.nii.gz. The
> subregion segmentation prior to trac-all -prep was successful and
> mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
> and other Thalamic Nuclei files were generated. In the archives I saw two
> others have experienced a similar issue without a resolution in the
> thread.
>
> I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6. I have
> attached the log file, log error, and my configuration file.
>
> Any help would be greatly appreciated!
>
> Thank you,
>
> Lauren Stephens
>
> *Lauren Stephens, MS *
>
> Assistant Clinical Research Coordinator
>
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
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--
----------------------------------------------------------------------------------------
Woo-Suk, Tae Ph.D. Research Professor
Brain Convergence Research Center, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: ws...@korea.ac.kr, woosuk....@gmail.com,
wo <woos...@naver.com>os...@gmail.com
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