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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