Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

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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