External Email - Use Caution Hello Anastasia,
The approach worked great and I was able to get the required TRACULA outputs from each step. According to the FreeSurfer Lookup Table, there are thalamic parcellation labels from 8001 - 8014. How can I access and visualize these thalamic labels? Thanks/Vinny On Thu, Sep 20, 2018 at 8:32 AM Vinny K <vinit.k.srivast...@gmail.com> wrote: > Thanks Anastasia, I'll give this approach a try. > > On Thu, Sep 20, 2018 at 8:31 AM Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > >> That's correct! You can source the setup script of whichever version you >> need to use. >> ------------------------------ >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Vinny K < >> vinit.k.srivast...@gmail.com> >> *Sent:* Thursday, September 20, 2018 8:25:31 AM >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] error with trac-all -prep >> >> >> External Email - Use Caution >> >> Hi Anastasia, >> >> Thanks for your reply. I needed the dev version in order to utilize the >> new thalamic segmentation nuclei tool: >> http://freesurfer.net/fswiki/ThalamicNuclei >> >> I'll download the stable one as well and use that one for Tracula. >> >> I'm assuming I can have both the stable and dev versions installed and >> modify the .bashrc profile to point to the correct freesurfer version that >> I wish to use? >> >> Vinny >> >> On Thu, Sep 20, 2018 at 8:20 AM Yendiki, Anastasia < >> ayend...@mgh.harvard.edu> wrote: >> >> Hi Vinny - Unless there was a specific reason why you were using a dev >> version (a feature that you needed and wasn't working in the stable one), >> please use the stable one in general. >> >> >> Best, >> >> a.y >> ------------------------------ >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Vinny K < >> vinit.k.srivast...@gmail.com> >> *Sent:* Thursday, September 20, 2018 6:57:02 AM >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] error with trac-all -prep >> >> >> External Email - Use Caution >> >> Hi Anastasia, >> >> A similar post had encountered a similar problem a while back: >> >> >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046979.html >> >> Should I install the latest stable release of FreeSurfer and run only the >> trac-all -prep step using the stable FreeSurfer release? Or should I >> repeat entire process starting with recon-all using the stable release? >> >> Thanks, >> >> Vinny >> >> On Wed, Sep 19, 2018 at 8:44 PM Yendiki, Anastasia < >> ayend...@mgh.harvard.edu> wrote: >> >> Hi Vinny - This error is during the diffusion-to-structural registration. >> Can you send the entire log file (scripts/trac-all.log)? >> >> Best, >> a.y >> >> On Sep 19, 2018 8:39 PM, Vinny K <vinit.k.srivast...@gmail.com> wrote: >> >> External Email - Use Caution >> >> Hi, >> >> I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4. >> >> I get the following error when running the command: trac-all -prep -c >> dmrirc. >> >> Any help would be greatly appreciated. >> >> Thanks, >> >> Vinny >> >> /home/Vinit/freesurfer/subjects/diffusion/Subj1 >> flirt.fsl -ref >> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii >> -in >> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii >> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz >> -90 90 -verbose 0 -omat >> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat >> -schedule /home/Vinit/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init >> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat0 >> Wed Sep 19 20:29:11 DST 2018 >> /home/Vinit/freesurfer/subjects/diffusion/Subj1 >> flirt.fsl -ref >> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii >> -in >> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii >> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz >> -90 90 -verbose 0 -omat >> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat >> -init >> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat >> -schedule /home/Vinit/freesurfer/bin/flirt.newdefault.20080811.sch >> terminate called after throwing an instance of 'NEWMAT::SingularException' >> Abort (core dumped) >> ERROR: flirt >> Linux LAPTOP-VTQVHSSF 4.4.0-17134-Microsoft #285-Microsoft Thu Aug 30 >> 17:31:00 PST 2018 x86_64 x86_64 x86_64 GNU/Linux >> >> trac-preproc exited with ERRORS at Wed Sep 19 20:29:14 DST 2018 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >
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