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 <laurenss@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: laurenss@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: wstae@korea.ac.kr, woosuk.tae@gmail.com, 
          woostae@gmail.com
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