Date: Tue, 27 Aug 2013 12:31:09 -0400
From: fischl@nmr.mgh.harvard.edu
To: pablonajt@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach Failure Detection

yes, definitely. The dicoms are best
On Tue, 27 Aug 2013, pablo najt wrote:
 
> Thank you very much for your input. Yes, I did start with analyze format and also I have visually inspected the images. Almost all my
> scans consistently show an extended whole in the prefrontal area (with a few exception of some scans showing this in posterior
> locations). 
> I am assuming the best is to start with either DICOM or NIFTI and avoid analyze format. Is this correct?
> 
> Best,
> Pablo
>   
> 
> Date: Tue, 27 Aug 2013 12:08:22 -0400
> From: fischl@nmr.mgh.harvard.edu
> To: pablonajt@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Talairach Failure Detection
> 
> Hi Pablo
> 
> have you visually inspected the talairach xform to see if it is indeed 
> incorrect? What input format did you start with? Most of these occur 
> because people start with analyze, which doesn't have the direction 
> cosines, and so the data is oriented incorrectly
> 
> cheers
> Bruce
>
> 
> On Tue, 27 Aug 2013, pablo najt wrote:
> 
> > Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a
> > macbook pro with snow leopard version 10.6.8. 
> > 
> > I would greatly appreciate if you could advise me which step/s should I take to correct this.
> > Thank you for your attention,
> > Pablo
> > 
> > Error:-------------------------------------------------------------------------------------------------------------------------------
> -
> > ------------------
> > #@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013
> > /Users/pablonajt/subjects/tr5713/mri
> > \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050)
> > 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
> > Darwin Pablo-Najts-MacBook-Pro.local 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 tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
> > 
> >
> 
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