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Freesurfer experts,
I have two MRIs for a patient separated by 5 years. I would like to look at progression of atrophy. These MRIs are different, however, firstly in terms of resolution (new one is 1x1x1, old one is 1.05x1.05x1.2), and secondly just in terms of general contrast, as they are different protocols from different scanners.
First I ran Freesurfer 6.0.0 on both MRIs; but the results I obtained didn't make much sense -- when I compared to a group of controls, the thickness values were much lower in the old MRI than in the new one. This could, of course, be due to variance in contrast / type of scanner, etc. Reviewing the surfaces, in both cases (old and new), all surfaces looked very good with no major errors.
I wanted to see how well the surfaces lined up over time -- so I wanted them in the same space. To get this, I co-registered the new MRI to the old one (via SPM), and re-ran recon-all on it. Now, when I compare to a group of controls, the new MRI has much more expected results -- e.g. lower thickness than the old one. Again, surfaces looked very good.
All that changed is the space the MRI was in when I fed it into FS -- some slight variance from voxel resolutions aside, this gave very different results. I looked at the lh.aparc.stats files and computed some percent differences and was pretty surprised by what I saw. For example, GrayVol values were different by 20% in the precentral, thickaverage was off by 17% in the precuneus.
obviously I made an error somewhere that caused this type of variance but I can't find it -- is there any advice for comparing this type of longitudinal data ?
thank you for any help you can provide!
Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003tel:713-363-9003
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