Thank you Bruce!

If I understand you correctly, would the command be

Recon-all -s subj_name -FLAIRpial.nii ?

Or would I first have to do recon-all with only T1 as input and then do another command after it has finished running? And in that case, what would that command be?

Best,
Vilde

Date: Wed, 8 Oct 2014 11:56:51 -0400
From: fischl@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs

Hi Vilde
 
no, you can't give recon-all a flair directly, it needs a  T1 do do the 
recon on. You use the flair at the end to do a post-hoc deformation using 
-flairpial I believe
 
cheers
Bruce
 
 
On Wed, 8 Oct 2014, Vilde wrote:
 
> Dear mailing list,
> I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for
> pial surface refinement. This results in an error message saying the
> dimensions are mismatched. (The third dimension of the T1 and Flair are
> different by one slice. ) I do not, however, have a problem running
> recon-all with only one T1 input. I am using Freesurfer v 5.1 .
> 
> I read in the release notes that in version 5.2 you can use the flag -FLAIR
> when you are using a flair image as input. I suppose this will not run in an
> earlier version? 
> Would it be correct to use the following  command :
> 
> recon-all -s [subject] -i T1.nii -i flair.nii -all
> 
> Kind regards,
> Vilde
> 
> 
>

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