External Email - Use Caution        

Hi FreeSurfers, 

I wanted to follow up on my post.  I am still receiving this error when running the preprocessing step of TRACULA.  We have run our files without the thalamic nuclei included, however, that is not ideal because we are interested in tracts that end nearby.  

I believe this is a bug in the code because otherwise the following TRACULA steps run all the way through with no error.  

If you have any suggests we would really appreciate it!

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


From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lauren Stephens <laurenss@stanford.edu>
Sent: Friday, October 6, 2023 7:41 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz
 

        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