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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
