External Email - Use Caution Hi Anastasia,
Thanks for your reply and your recommendation to use mri_binarize to set up ROIs. Actually, I was able to use the new thalamic tool Eugenio had set up with good segmentation. It's just that I had noticed thalamic labels in the FreeSurfer LUT and I thought these were specific TRACULA outputs, i.e., thalamic parcellation based on diffusion connectivity. Vinny On Tue, Sep 25, 2018 at 8:33 AM Yendiki, Anastasia <ayend...@mgh.harvard.edu> wrote: > 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> > 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. >>> >> _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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