Could it be that since we skip motioncor, we skip the mri_add_xform_to_header program as well? Should I be running that separately?
Thanks, Erin Browning On Fri, Jun 7, 2013 at 11:54 AM, Erin Browning <[email protected]> wrote: > Hi Doug-- > > Running: > > recon-all -s freesurfer -autorecon2 -autorecon3 > > produced the same error. Could you send me the new version of the program? > > Thanks! > Erin Browning > > > On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve <[email protected] > > wrote: > >> >> OK, this is a known problem when running recon-all with -autorecon1 >> -autorecon2 but not autorecon3. If you run it with -autorecon3, then it >> should run all the way through without a problem. Alternatively, I can >> give you a new version of the offending program (mri_segstats) that will >> allow you to use just ar1 and ar2. >> >> doug >> >> >> >> >> On 06/06/2013 03:46 PM, Erin Browning wrote: >> > Here is the log file. >> > >> > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=zrh2oi9> >> > >> > Thank you! >> > >> > >> > On Thu, Jun 6, 2013 at 2:43 PM, Erin Browning <[email protected] >> > <mailto:[email protected]>> wrote: >> > >> > Yes, it was. I tried copy and pasting it and just attaching the >> > log file. Can I paste urls here? I'll just upload it to pastebin >> > or something like that. >> > >> > >> > On Thu, Jun 6, 2013 at 2:38 PM, Douglas N Greve >> > <[email protected] <mailto:[email protected]>> >> wrote: >> > >> > That's weird, people upload their recon-all.log files all the >> > time. Was >> > the email kicked back to you? >> > >> > On 06/06/2013 03:27 PM, Erin Browning wrote: >> > > The log file for recon-all is too large. How should I send it? >> > > >> > > >> > > On Thu, Jun 6, 2013 at 1:48 PM, Douglas N Greve >> > > <[email protected] >> > <mailto:[email protected]> >> > <mailto:[email protected] >> > <mailto:[email protected]>>> wrote: >> > > >> > > Hi Erin, thanks for reposting. Can you post the >> > recon-all.log file? >> > > doug >> > > >> > > >> > > On 06/06/2013 02:37 PM, Erin Browning wrote: >> > > > Hi everyone-- >> > > > >> > > > I emailed the other day about hyperintensity after >> running >> > > motioncor. >> > > > We've skipped motioncor in our processing now, but we >> > keep getting >> > > > this error while running AR2. >> > > > >> > > > \n mri_ca_register -invert-and-save >> > transforms/talairach.m3z \n >> > > > mri passed volume size is different from the one used >> > to create >> > > M3D data >> > > > Loading, Inverting, Saving, Exiting ... >> > > > Reading transforms/talairach.m3z >> > > > gunzip -c transforms/talairach.m3z >> > > > Inverting GCAM >> > > > ERROR: mri_ca_register with non-zero status 0 >> > > > Darwin cerebrum.uwm.edu <http://cerebrum.uwm.edu> >> > <http://cerebrum.uwm.edu> >> > > <http://cerebrum.uwm.edu> 10.8.0 Darwin Kernel >> > > > Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; >> > > > root:xnu-1504.15.3~1/RELEASE_I386 i386 >> > > > recon-all -s freesurfer exited with ERRORS at Wed Jun 5 >> > > 19:32:56 CDT 2013 >> > > > >> > > > I tried rerunning recon-all -s freesurfer -talairach >> > before running >> > > > AR2, and that didn't fix the error. What's going wrong? >> > > > >> > > > Thanks, >> > > > Erin Browning >> > > > >> > > > >> > > > >> > > > _______________________________________________ >> > > > Freesurfer mailing list >> > > > [email protected] >> > <mailto:[email protected]> >> > > <mailto:[email protected] >> > <mailto:[email protected]>> >> > > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > -- >> > > Douglas N. Greve, Ph.D. >> > > MGH-NMR Center >> > > [email protected] <mailto:[email protected]> >> > <mailto:[email protected] >> > <mailto:[email protected]>> >> > > Phone Number: 617-724-2358 >> > > Fax: 617-726-7422 >> > > >> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > > >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > > Outgoing: >> > > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > [email protected] >> > <mailto:[email protected]> >> > <mailto:[email protected] >> > <mailto:[email protected]>> >> > > 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 >> > > [email protected] >> > <mailto:[email protected]> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > [email protected] <mailto:[email protected]> >> > Phone Number: 617-724-2358 >> > Fax: 617-726-7422 >> > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > Outgoing: >> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > [email protected] >> > <mailto:[email protected]> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > [email protected] >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [email protected] >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >
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