External Email - Use Caution
Hi Lauren. Would you send me the trac-preproc ( /your path to/freesurfer/bin ) file, you corrected?
best regards
Woo-Suk, Tae
On Tue, Oct 31, 2023 at 4:29 AM Lauren Stephens laurenss@stanford.edu wrote:
External Email - Use CautionHi Woo-Suk,
I was able to make the change however, I am still receiving the same error.
mri_convert -at /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz
mri_convert -at /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz
reading from /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz...
error: niiRead(): error opening file /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version 22.6.0: Fri Sep 15 13:39:52 PDT 2023; root:xnu-8796.141.3.700.8~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Oct 30 12:24:56 PDT 2023
Do you have any further suggestions to fix this issue?
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 Woo-Suk Tae < woostae@gmail.com> *Sent:* Saturday, October 28, 2023 10:34 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz
External Email - Use CautionHi, 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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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, wo woostae@naver.comostae@gmail.com
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