João, As Bruce said different cohort produce different results. You should expect a thinning in superior temporal, in enthorrinal cortex. Sometimes in AD I haven't found thinning in parietal cortex.
But I think you should compare your cohort with the published data with AD and cortical surface analysis (I have an annotated bibliography I can share) Best Regards, Pedro Paulo Jr. 2008/10/5 Bruce Fischl <[EMAIL PROTECTED]> > Hi Joao, > > previous bias correction should be fine, and previous skull stripping (if > it's accurate) should as well, assuming you understand the recon-all stream > well enough to get into it at the right place. > > As for the false negatives, can you tell us something about your data? What > stage of AD? What are you comparing to? We've processed a *ton* of AD data > and have seen different things in different cohorts, but some basic patterns > repeated. > > cheers, > Bruce > > > > On Sun, 5 Oct 2008, Joao Pereira wrote: > > Pedro, >> >> Thanks for your reply. >> >> By false negatives I mean a lack of detection of atrophic areas which I >> know >> are present in this AD cohort, namely the parietal convexities. I'm unable >> to visualise them with FS. >> >> Finally, you've recommended me not to seed anything to recon-all which had >> been skull stripped. Is there any way of going around this? And what about >> data which had been previously bias corrected? >> >> Thank you very much for all you help! >> >> Best, >> >> Joao >> >> -----Original Message----- >> From: [EMAIL PROTECTED] >> [mailto:[EMAIL PROTECTED] Behalf Of Pedro Paulo >> de >> Magalhães Oliveira Junior >> Sent: 03 October 2008 21:25 >> To: Joao Pereira >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Voxel resolution impact / skull stripping and >> biascorrection replacement >> >> >> João, >> >> >> Here is my opinion: >> >> >> I have worked on resolutions distinct than 1mm3 isotropic and usually I >> have no problem. What do you mean by false negatives in your cohort study? >> >> >> I think you should avoid seeding data with skull striped by other program >> to the pipeline. >> >> >> Best Regards, >> >> >> PPJ >> >> >> >> 2008/10/3 Joao Pereira <[EMAIL PROTECTED]> >> >> Hello, >> >> I have a couple of questions on which I would like to have your opinion. >> >> The first is the voxel resolution impact on cortical thickness >> sensitivity. >> I'm using 1.25 mm3 isotropic voxels, and I know that FS interpolates >> scans >> to 1mm - is it possible that the 1.25 mm resolution hinders cortical >> thickness measurements? I'm asking this because I'm analysing an AD >> cohort >> whose result seems full of false negatives (I'm in the process of >> inspecting >> the intermediate steps as well - I just wanted to check if resolution >> was a >> factor as well). >> >> I would also like to know if it is possible (and advisable) to input >> already >> optimally skull stripped and bias corrected brains into the recon-all >> pipeline. If that is possible, I would assume that I need to bypass >> those >> steps, and I would like to know which arguments to use in recon-all in >> order >> to do so. >> >> Thank you very much for all your help! >> >> Best, >> >> Joao Pereira >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> -- >> ----------------------------------------------------------- >> Pedro Paulo de M. Oliveira Junior >> Diretor de Operações >> Netfilter & SpeedComm Telecom >> >> -- ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom
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