Hi Bruce.

After I talked to you, the error changed from what I said to something else as it looks like the recon-all executed further. It looks like it overwrote our *.out log which captures the output coming to the terminal. I’ve included an out.old which shows the original error. The new error is about avi2talxfm failing. I’ve enclosed the talairach_avi.log as it suggested as well as some other logs I thought might be helpful. Let me know if you need any other info. I wanted to include the talairach.xfm file, but that does not seem to exist anymore.

Thanks for your help. -John

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of West, John D. Sent: Monday, August 19, 2013 12:07 AM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach error - Talairach file seems to not be written correctly.

Hi Bruce.

Not that I can see. And it did create the talairach.xfm, but that file is missing the header for some reason. I'll send the log just as soon as I'm in tomorrow and I'll include the xfm file as well.

Thanks so much for the help. -John

Sent from my Windows Phone ________________________________ From: Bruce Fischlmailto:fischl@nmr.mgh.harvard.edu Sent: ‎8/‎18/‎2013 10:08 PM To: West, John D.mailto:jdwest@iupui.edu Cc: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach error - Talairach file seems to not be written correctly. Hi John

can you send the entire recon-all.log? Any indication why the talairach.xfm was not created?

cheers Bruce On Sun, 18 Aug 2013, West, John D. wrote:

Hello.

We are trying to run freesurfer on a Super Computing system here at IU. Unfortunately, we keep running into the following error:

#-------------------------------------------- #@# Talairach Failure Detection Sun Aug 18 14:17:32 EDT 2013 /N/dc/projects/shenlab/subjects/10025_5/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ltMNIreadEx:transforms/talairach.xfm does not start as 'MNI Transform File' ERROR: talairach_afd::Load_xfm(): could not parse transforms/talairach.xfm Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux nid00170 2.6.32.59-0.7.1_1.0401.6845-cray_gem_c #1 SMP Thu Nov 15 00:24:59 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 10025_5 exited with ERRORS at Sun Aug 18 14:17:37 EDT 2013

For more details, see the log file /N/dc/projects/shenlab/subjects/10025_5/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The talairach file shows this:

1.059250 0.121638 -0.012966 -0.232872 -0.118758 0.992805 0.165794 -34.672363 0.032261 -0.111376 1.084429 -0.219055;

Note, the file does not have the typical header. We've run this same subject on other systems with no issue. Is there any reason the header would not be written?

Any help would be greatly appreciated.

Thanks. -John West Systems Administrator IU Center for Neuroimaging _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.