From fischl@nmr.mgh.harvard.edu Wed Feb 23 18:44:08 2011
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Subcortical segmentation of a	skull-stripped
 Analyze-formatted image
Date: Wed, 23 Feb 2011 18:44:08 -0500
Message-ID: <Pine.LNX.4.62.1102231843560.1157@gate.nmr.mgh.harvard.edu>
In-Reply-To: <1298498229.7873.35.camel@terrier.nmr.mgh.harvard.edu>
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does the orig.mgz show up properly in tkmedit?
On Wed, 23 Feb 2011, Nick 
Schmansky wrote:

> 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, andrewkrause(a)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
>> _______________________________________________
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>> Freesurfer(a)nmr.mgh.harvard.edu
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>>
>>
>
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