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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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