It fails before ar3 runs.
There is no indication in this log file that you ran autorecon3
doug
On 06/07/2013 02:51 PM, Erin Browning wrote:
Here's the log. I ran mri_add_xform_to_header after it failed again last time and am currently rerunning AR2+3 on it, so you can probably ignore the latest modifications to it.
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=iowkgmv
We're running Mac OSX 10.6.8.
Thanks,
Erin
On Fri, Jun 7, 2013 at 12:22 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
Hmmm, I don't know. I think that something strange is happening.
Can you
send me the new recon-all.log file? Also, tell me what platform
you are
using and I'll send you a new version of mri_segstats
doug
On 06/07/2013 01:14 PM, Erin Browning wrote:
> 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 <brownin8@uwm.edu
<mailto:brownin8@uwm.edu>
> <mailto:brownin8@uwm.edu <mailto:brownin8@uwm.edu>>> 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
> <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@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
> <brownin8@uwm.edu <mailto:brownin8@uwm.edu>
<mailto:brownin8@uwm.edu <mailto:brownin8@uwm.edu>>
> > <mailto:brownin8@uwm.edu <mailto:brownin8@uwm.edu>
<mailto: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>
> <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
> <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
> <mailto: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>>
> > <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
> > <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto: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>
> > <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>>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > <mailto: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>>
> <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
> > <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto: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>
> > <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>
> >
> <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>>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > <mailto: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>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > <mailto: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>>
> <mailto: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>
> > <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>
> >
> <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>>
> > <mailto: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
> >
> >
> >
> >
> >
> > _______________________________________________
> > 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
>
>
>
>
>
> _______________________________________________
> 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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/