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Hi Bruce,
No, I don’t think that you’ve misunderstood. I was asking about cohorts
that had not been visually inspected in my first message and then in my
last message I wanted to check that I didn’t need to also remove people
from visually inspected data based on statistical outliers (as a further
step). In conclusion, from what I’ve understood: if there is no visual
inspection of data, it is best to remove statistical outliers (based on
standard deviations) even for global measures such estimated intracranial
volume, mean thickness from left and right hemispheres. When data is
visually inspected, there is no need to remove any data based on
statistical outliers even if those exist as these should be good quality.
For the visual inspected data, I have kept all participants (which have an
acceptable cortical surface reconstruction rating) for the regional
variables and I also retained all participants for global measures
(thickness of mean hemisphere, estimated intracranial volume) as the data
had been processed and removed from further Freesurfer processing if they
had severe artifacts or irregularities.
Many thanks for your advice.
On Thursday, November 19, 2020, Fischl, Bruce <bfis...@mgh.harvard.edu>
wrote:
> Hi Stephanie
>
>
>
> Sorry, I think I misunderstood. If you have visually inspected the
> analysis results and think that they are accurate then you definitely
> should leave those subjects in
>
>
>
> 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 4:19 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Mean thickness estimation {Disarmed}
>
>
>
> * 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!
>
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