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<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.
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