External Email - Use Caution 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 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.
