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 <gr...@nmr.mgh.harvard.edu>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 <brown...@uwm.edu > > <mailto:brown...@uwm.edu>> 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 > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > 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 > > > <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> 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 > > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>> > > > 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 > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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 > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > 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 > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > 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 > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
_______________________________________________ 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.
