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 <fis...@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 > > > > > _______________________________________________ > 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. > >
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