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Hi Woo-Suk,
The change you suggested did work when i made a second attempt. The files were getting mixed in with the trac-preproc copy I created in case of errors.
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: Monday, October 30, 2023 8:48 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz
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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.edumailto:laurenss@stanford.edu> wrote:
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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.eduhttp://secure-web.cisco.com/1hfiYFGQhzjFVnZavl-fTMAJOa_JE9bzjVA8nrzYF3yRbWe4VzGqfDesdrYhWYxOR5nsphpAwt1gyWvjHUHQdWEiA9qbrEWmQFdrmnEbo5BDDYjQ6O-KnWv9c1QD7bhdcX5EzX6HzbBIFX0ir6HvpcK-2VMbNvy-cC26PgUPAXxjO_gI43uMjUhPyKeIEY1j_k9KKcxCGxdVYQrCLxLSs0xrHxxEIjtuNcmEEMkiviG30UZwoYYCAL2B9dYpccBFZ_PcMy-xXHxsefxUDMgA-ehOWri2bOrXsubbsWH6K3u6VLMCziEZcNfVMRF2yYF4_/http%3A%2F%2FPSYC-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.edumailto:laurenss@stanford.edu
P: (650)-725-1716
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Woo-Suk Tae <woostae@gmail.commailto:woostae@gmail.com> Sent: Saturday, October 28, 2023 10:34 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz
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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.edumailto:laurenss@stanford.edu> wrote:
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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.edumailto: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.krmailto:wstae@korea.ac.kr, woosuk.tae@gmail.commailto:woosuk.tae@gmail.com, womailto:woostae@naver.comostae@gmail.commailto:ostae@gmail.com ----------------------------------------------------------------------------------------
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---------------------------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Korea University College of Medicine, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6077 email: woosuk.tae@gmail.commailto:woosuk.tae@gmail.com, wmailto:woosuk.tae@kumc.or.krstae@korea.ac.krmailto:stae@korea.ac.kr woostae@naver.commailto:woostae@naver.com ----------------------------------------------------------------------------------------