Hi Vinny - Glad that things worked out. I'll defer to Eugenio about the thalamic parcellation, but in general mri_binarize --match allows you to create an ROI from all the voxels in a segmentation map that have a specific segmentation ID.
a.y On Sep 25, 2018 7:33 AM, Vinny K <vinit.k.srivast...@gmail.com> wrote: 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<mailto: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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Vinny K <vinit.k.srivast...@gmail.com<mailto:vinit.k.srivast...@gmail.com>> Sent: Thursday, September 20, 2018 8:25:31 AM To: freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Vinny K <vinit.k.srivast...@gmail.com<mailto:vinit.k.srivast...@gmail.com>> Sent: Thursday, September 20, 2018 6:57:02 AM To: freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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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