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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1mbZ6TiwAjZyXHWt0vWwUF4mmwAlMoO41mwD4m80I0xkM0yxR3a_Z7YeDCGNXtP3wyVlhdxN0ChbZDaAjEuhQoghPYxMAJSteUSqeB7MF4-L0Tf8FsDLFXiWNz-KnU-re_mqlz-AXa2mAnoH8hvKI6IJ23ANyNMGBis5RO1oMhTy5yDaI833kgeGvPVzrc3UXngF13YAI3utqkrkb0ssut4jifFVnS-uAlo1HkadPcWDYYEsre38v2YeJ7XQTOanc719223QJmCY28ugu02PGBxFplISpgGt8DWtq6RSKnosmxtFNVPUXPLSCWLjQ8b1R/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > -- ---------------------------------------------------------------------------------------- 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 ----------------------------------------------------------------------------------------
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.