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Hi Bruce,
Is it also necessary to remove outliers (eg. 3 SD from the mean) for Freesurfer structural measures of MRI images that have been visually inspected as a further data cleaning step?
I really appreciate your help.
Thanks
On Thu, Nov 19, 2020 at 3:55 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Stephanie
I think that is always a good idea, unless for some reason it isn’t possible
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Stephanie K *Sent:* Thursday, November 19, 2020 2:14 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Mean thickness estimation
External Email - Use Caution *Hi Bruce,
Thanks for the prompt reply. It is my understanding that l_thickness, r_thickness and estimated intracranial volume are accurately measured. Would I still need to identify and remove outliers if visual inspection of the images has not been done?
Many thanks,
Stephanie
On Wed, Nov 18, 2020 at 5:24 PM Stephanie K rklinden@gmail.com wrote:
Hi,
I want to estimate the mean cortical thickness. For this I have summed the thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, I also have the average mean thickness of left and right hemispheres (direct output variables of Freesurfer). As there is no visual inspection of the imaging in the particular cohort, I remove measures that are 3 standard deviations above or below the mean. Hence, I may expect more outliers to be removed when I take the average across the regions. I am using these brain measures as outcomes in association analyses with the genetic score as the exposure. For the mean thickness (averaged across the left and right hemisphere thickness variables of freesurfer after removing outliers), the regression coefficients have a smaller standard deviation than with thickness averaged across the 34 regions. I’m not sure which one to use - which one is more accurate? When I look at the mean thickness (which I derived using 34 regions) and it’s standard deviation, it is similar to that of the average mean thickness across the two hemispheres as well as the standard deviation of that. Can you suggest what is most accurate please and what the difference is between the mean thickness across the two hemispheres obtained from freesurfer and those calculated across the regions? Why does one result in more precision than in the other?
Thank you!
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