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>
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 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>
> 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
>
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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, woosuk....@gmail.com,
> wo <woos...@naver.com>os...@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....@gmail.com, w <woosuk....@kumc.or.kr>s...@korea.ac.kr
woos...@naver.com
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