add the flag -notal-check to the end of recon-all command to skip the
check.   

if you can make your average using nifti format you're better off as
analyze doesnt retain orientation (l/r) info.

you may have to manually register the brain following this:
 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

n.


On Wed, 2011-02-23 at 13:38 -0800, andrewkra...@ucla.edu wrote:
> Hello,
> 
> I'm a complete newbie to FreeSurfer, so I appreciate any and all help  
> you can provide. I am trying to use FreeSurfer to automatically create  
> some masks of subcortical structures, but am having trouble getting  
> the whole process started.
> 
> When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is  
> my subject name) it quits with the error
> 
> "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm  
> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)"
> 
> 
> I am trying to do this to a skull-stripped brain originally in Analyze  
> format (there are no DICOMs since it's actually an average of many  
> skull-stripped scans), to which I've already registered all of the  
> scans I want to study. I used mri_convert to convert the .img file  
> into a .mgz file, but compared to the bert example, the background  
> (non-brain area) is a light gray instead of black. I don't know if  
> this is where the error is occuring, and if it is, how to correct it.  
> If it helps, the scan I'm trying to create masks from has been  
> registered to the ICBM brain template.
> 
> Let me know what other information you need and thanks for the help,
> -- Andrew
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 

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