External Email - Use Caution 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 <bfis...@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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@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 <rklin...@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! > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1KPUR-tLJEURgzYmremNK46BwlQzhr2HuE-Vgj0d_IfX_gecAUGN6QjCWYLIn3brTZNmVndmFck4JXbECP-4ChBCCB9on11GCIcDXo_CeNsBG78TW3Un3dAkQZk9obRuWPnrYHXzp4kS7t-Y4GsaRBH04naRD0rppbxKez7XlIyHvl1NMwlQaEMRHOk6FqYoTIVHV6UrlC5oR6DZFRClnWLATwzWDCvj5zCYsdJ7pt7xmr1fz3Jml3iS6BjOivmfV4vWBZ-x-rpFZ_zoHRv07WA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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