I Ismail

yes, if you have juxtacortical lesions you should label them as such in
the aseg, then I think it should work

cheers
Bruce
On Fri, 9 Dec 2016, Ismail Koubiyr
wrote:

> Dear Freesurfer experts,
> We are facing a problem in our study and would need your advice on it.
> We want to get an accurate measurement for the cortical thickness from our
> MS patients data. For that we are using 3D T1 and FLAIR (recon-all will be
> used with the FLAIR option so that we can a more accurate pial surface).
> However, we were wondering if running recon-all on the raw data would lead
> to some errors specially because of the juxtacortical lesions or not. Or, is
> it better to first apply a lesion filling using our lesion mask ?
> I should specify that we will use the longitudinal pipeline if it is of any
> use.
>
> Thank you all.
>
> Ismail
>
> PhD candidate
> Neurocentre Magendie, INSERM
> Bordeaux, France
>
>

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