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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