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 Fischl
Sent: ý8/ý18/ý2013 10:08 PM
To: West, John D.
Cc: 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
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>
>
>


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