New subject: Surface Area in Toddlers/Children {Disarmed}

12 Aug 2018

      The flag to preserve area is not being turned on there. You can try 
running mris_preproc separately for area and including the --jac flag. 
If that does not work, you can download version6 and just use it to run 
mris_preproc
On 8/10/18 4:41 PM, Derek Sayre Andrews wrote:
...
External Email - Use Caution
Hi Douglas,
Of course, please find attached a copy of the recon-all.log file.
Best, Derek
PS: Apologies for the direct email in order to get you the attachment
cid:image001.png@01D430A0.A5153C80
*Derek Sayre Andrews, PhD*
Postdoctoral Scholar
Department of Psychiatry and Behavioral Sciences
The M.I.N.D Institute
University of California Davis
Telephone: +1 916 703 0360
Email: dandrews@UCDavis.edu mailto:dandrews@UCDavis.edu
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas 
Greve dgreve@mgh.harvard.edu
*Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu
*Date: *Friday, August 10, 2018 at 11:12 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
*Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children
Yes. -qcache actually calls mris_preproc. At one point, FS did not 
preserve total area when  mapping to fsaverage. I fixed it a while 
ago, but maybe something was still off in 5.1
On 8/10/18 2:06 PM, Derek Sayre Andrews wrote:
*        External Email - Use Caution *

Hi Douglas,

Thank you for the response.

I did not use mris_preproc to prepared the data.

The data was mapped to fsaverage using recon-all with -qcache. I
then loaded the l/rh.area.pial.fwhm15.fsaverage.mgh files into
MATLAB using SurfStatReadData
<http://www.math.mcgill.ca/keith/surfstat/> and summed them across
each vertex.

Would the terminal output of recon-all -qcache be helpful?

Best, Derek

cid:part2.2B5BCEFF.1D6DDEE5@mgh.harvard.edu

*Derek Sayre Andrews, PhD*

Postdoctoral Scholar

Department of Psychiatry and Behavioral Sciences

The M.I.N.D Institute

University of California Davis

Telephone: +1 916 703 0360
Email: dandrews@UCDavis.edu <mailto:dandrews@UCDavis.edu>

*From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
Douglas Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Friday, August 10, 2018 at 10:25 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children

It should be preserving total surface area. Can you send your
mris_preproc command line and the terminal output? It might be
something with 5.1 as well.

On 8/9/18 3:49 PM, Derek Sayre Andrews wrote:

    *        External Email - Use Caution *

    Dear Freesurfer Developers and Experts,

    I have been exploring various vertex wise (mass univariate)
    effects using freesurfer measures of cortical thickness and
    surface area in a cohort of toddlers/children aged 25-70 months.

    When looking at the effect of age on surface area using
    individuals’ measures mapped to fsaverage and smoothed at 15mm
    fwhm (area.pial. fwhm15.fsaverage.mgh) I observed a widespread
    negative effect of age (i.e. decreased surface area with age).
    Given the age group of the cohort this seems implausible.
    Plotting the sum of each individuals
    lh+rh.area.pialfsaverage.fwhm15.mgh against age shows the
    relationship:

    cid:image001.png@01D42FCE.C197B360

    However, plotting the lh+rh total surface area returned by
    mris_anatomical_stats reveals a much more plausible
    relationship between surface area and age:

    cid:image002.png@01D42FCE.C197B360

    My working hypothesis is that the significantly smaller brain
    sizes of our cohort compared to fsaverage, and the fact(?)
    that -qcache does not preserve global surface area, is causing
    an “over adjustment” in our cohorts smallest brains when
    mapped to fsaverage.

    Thus, my questions are three fold

     1. Is the mapping of our significantly smaller brains to
        fsaverage a potential explanation for the results we are
        seeing in our mass univariate analyses of surface area?

     2. If this is the case, would this effect be limited to
        surface area or also extend to other freesurfer measures
        including cortical thickness, lGI, sulcal depth etc.

     3. How would you recommend approaching vertex wise analyses
        in a cohort of this age? Create a study specific average
        subject using make_average_subject to map onto?

    Thank you for your insight and guidance!

    Best, Derek

    PS: All processing was performed using freesurfer v5.1

    cid:image003.png@01D42FCE.C197B360

    *Derek Sayre Andrews, PhD*

    Postdoctoral Scholar

    Department of Psychiatry and Behavioral Sciences

    The M.I.N.D Institute

    University of California Davis

    Telephone: +1 916 703 0360
    Email: dandrews@UCDavis.edu <mailto:dandrews@UCDavis.edu>

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