Alright, thanks a lot for your help Bruce. Best,
Ismail PhD candidate Neurocentre Magendie, INSERM Bordeaux, France 2016-12-12 17:33 GMT+01:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > 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 <fis...@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 < >> 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. >> > >> > >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > _______________________________________________ > 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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