because filling in the T1 may cause artifacts

On Mon, 12 Dec 2016, Ismail Koubiyr wrote:

Would you please give me the reasons why the former would be better ?
Ismail

PhD candidate
Neurocentre Magendie, INSERM
Bordeaux, France


2016-12-12 15:47 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
      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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