On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve <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>> 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
>
>
>
>
>
> _______________________________________________
> 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
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/

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