External Email - Use Caution
Hi 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: laure...@stanford.edu
P: (650)-725-1716
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Woo-Suk Tae
<woos...@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 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<mailto: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<mailto:laure...@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: ws...@korea.ac.kr<mailto:ws...@korea.ac.kr>,
woosuk....@gmail.com<mailto:woosuk....@gmail.com>,
wo<mailto:woos...@naver.com>os...@gmail.com<mailto:os...@gmail.com>
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