Thank you Doug,

Attched are to snapshots

#1 is for the original T1 ( i.e. as aquired) and this image what output the error message mentioned in my previous email.

#2 is after correcting the orientation using the command "fslswapdim 001.nii RL PA IS T1-2mm_orientOK.nii"

I re run the same command "recon-all" on the newly corrected T1 image. The analysis is runnig fine right now, but when I checked the file "recon-all" I found similar error to what terminated my previous analysis. The differnce here is that the analysis didn't fail!

Here is what I have in "recon.log"

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0386, pval=0.0034 < threshold=0.0050)
INFO: Attempting MINC mritotal to perform Talairach align

Do I need to warry about this error? I appreciate any suggestion to improve analyzing this image.

Bests,
John

Sent: Friday, November 11, 2016 at 3:19 PM
From: "Douglas N Greve" <greve@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon all

This can also happen if the head is oriented in a strange way. This can
happen with older patients that tend to tilt their head back.

On 11/10/2016 08:27 PM, Bruce Fischl wrote:
> Hi John
>
> it means that the talairach transform that was computed was extremely
> unlikely and deemed to be probably incorrect. Frequently this happens
> if you start with images (like analyze) that don't contain accurate
> direction cosine information. You can check this by bringing one of
> the volumes in freeview and checking to make sure that the anatomical
> directions we show
> (e.g. anterior/posterior) correspond to the true anatomy. Sometimes
> abnormal anatomiies like huge ventricles can also make it fail, but
> you need to figure out which one it is before deciding what to do
>
> cheers
> Bruce
>
>
> On Fri, 11 Nov 2016, John Anderson wrote:
>
>> Dear Freesurfer experts,
>> I ran the following command on a T1 image
>> recon-all -subjid 089 -all -qcache
>>
>> and I got the following error message:
>>
>> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
>>
>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
>> ***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050)
>>
>>
>> I highly appreciate an explanation for the meaning of this error and
>> how to
>> fix it.
>>
>>
>> Best
>> John
>>
>>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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