9 Jun
2013
9 Jun
'13
5:50 a.m.
Hi Doug,
I had a similar problem when running recon-all with -autorecon1 & 2 flags, and I'd like to try to use a bug fixed mri_segstats.
How can I get the new version?
Thanks, Akio
(2013/06/07 5:01), Douglas N Greve 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%3E
Thank you!
On Thu, Jun 6, 2013 at 2:43 PM, Erin Browning <brownin8@uwm.edu mailto:brownin8@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
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