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 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
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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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 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 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/
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.
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> 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> 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> > 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you can also use
https://gate.nmr.mgh.harvard.edu/filedrop2/
On Thu, 6 Jun 2013, Douglas N Greve 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> 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 dataLoading, 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> 10.8.0 Darwin KernelVersion 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 2013I 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>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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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> 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> 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> > 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 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 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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
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> 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> 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 beforerunning
> 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> > 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 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 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug! I'll run it with AR2+AR3 from now on.
On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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 afterrunning
> 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 contactthe
> 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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 afterrunning
> 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 contactthe
> 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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
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 afterrunning
> 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 contactthe
> 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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> 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>> 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>>> 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>>> 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>>>> 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> 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>>> > > > > 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 > > > > > > 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>> > > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what is your platform?
On 06/09/2013 05:50 AM, Akio Yamamoto wrote:
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 Isend 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/BugReportinghttp://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
It's CentOS 6 x86_64.
Thanks, Akio
(2013/06/11 0:11), Douglas N Greve wrote:
what is your platform?
On 06/09/2013 05:50 AM, Akio Yamamoto wrote:
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 Isend 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/BugReportinghttp://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
try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos6
On 06/10/2013 04:33 PM, Akio Yamamoto wrote:
It's CentOS 6 x86_64.
Thanks, Akio
(2013/06/11 0:11), Douglas N Greve wrote:
what is your platform?
On 06/09/2013 05:50 AM, Akio Yamamoto wrote:
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.edumailto:greve@nmr.mgh.harvard.edu> wrote:
That's weird, people upload their recon-all.log files allthe 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 Isend 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/BugReportinghttp://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
freesurfer@nmr.mgh.harvard.edu
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Akio Yamamoto -
Bruce Fischl -
Douglas N Greve -
Erin Browning