the former I think, but it's an empirical question
Bruce

On Mon, 12 Dec 2016, Ismail Koubiyr wrote:

> Hi Bruce,
> Thanks for your answer.
> What do you think would be better, run recon-all on the original data (with
> lesions) then edit the aseg for the juxtacortical lesions or use a lesion
> filling on the T1 and then run recon-all on it.
> Thanks again.
>
> Cheers,
>
> Ismail
>
> PhD candidate
> Neurocentre Magendie, INSERM
> Bordeaux, France
>
> 2016-12-09 22:58 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
>       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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