you would have to first run recon-all -all on the T1
On Wed, 8 Oct 2014, 
Vilde wrote:
 
> 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 -FLAI
> R
> > 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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