External Email - Use Caution
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: 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: 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
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
<laure...@stanford.edu<mailto:laure...@stanford.edu>> wrote:
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<http://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: laure...@stanford.edu<mailto:laure...@stanford.edu>
P: (650)-725-1716
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Woo-Suk Tae <woos...@gmail.com<mailto:woos...@gmail.com>>
Sent: Saturday, October 28, 2023 10:34 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1l3bOcVVUOna_kRMjlbTD9_UI5MPlOthsxjoVQnTwUWVjaF2AvNvl17txA3jADORH1u_rUctFd9MY_AF19N3HjxgNv2OxA_ssTK849eg6LmDtTeIJLBCPqYW3YjtunsUzI-ob580eW6cEq0K3ItlAWH0UNu784U-t791eUAKj0_P30BatNzBiXlXx1uKY56swDhs5isYTtATQ_aBW5Y6gvBlvrH7fSj25AD73azt80A0ovX2u0QbLb3Axvb-gGkkgo_j_RKBiGuJuCJaqMFm2UeLM5AAHya2MEeTjKC66LagFhRpRE2c0c-y8LgwvJpNg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<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<mailto:ws...@korea.ac.kr>,
woosuk....@gmail.com<mailto:woosuk....@gmail.com>,
wo<mailto:woos...@naver.com>os...@gmail.com<mailto:os...@gmail.com>
----------------------------------------------------------------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1l3bOcVVUOna_kRMjlbTD9_UI5MPlOthsxjoVQnTwUWVjaF2AvNvl17txA3jADORH1u_rUctFd9MY_AF19N3HjxgNv2OxA_ssTK849eg6LmDtTeIJLBCPqYW3YjtunsUzI-ob580eW6cEq0K3ItlAWH0UNu784U-t791eUAKj0_P30BatNzBiXlXx1uKY56swDhs5isYTtATQ_aBW5Y6gvBlvrH7fSj25AD73azt80A0ovX2u0QbLb3Axvb-gGkkgo_j_RKBiGuJuCJaqMFm2UeLM5AAHya2MEeTjKC66LagFhRpRE2c0c-y8LgwvJpNg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1jsysVCI-hdZBfcsIdJ0SdbSI3Nhmea9kE6wDEb2pNW-LnsK8yE4zpaUvfC4oDCLTEGRbuJm2HlBf5tlzb7YhGOU0zcWpl_PSsejlTzAk5toKxCJxgdSTt3sUkPwpuBeCL0-zm3O4ZTDfwDuh0aZ3AmbFRfZIexCVr9i7FjzBZq56MuM0XN0vbYAwcKe6tZzij4TW2XEjg0pLvvMpv756o_EIqBXgFyTqdIbBRAs0272gvcYebjMFHLcDF3khd_VKD8qm6K0A-hVZSJTqQH9met_fl77QEiQGBxj2fBsl42EtTLq8g0R7nPxlzTRikmiQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
--
----------------------------------------------------------------------------------------
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....@gmail.com<mailto:woosuk....@gmail.com>,
w<mailto:woosuk....@kumc.or.kr>s...@korea.ac.kr<mailto:s...@korea.ac.kr>
woos...@naver.com<mailto:woos...@naver.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.
