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 CautionHi 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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