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
*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: dandr...@ucdavis.edu <mailto:dandr...@ucdavis.edu>
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
Greve <dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Date: *Friday, August 10, 2018 at 10:25 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" <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: dandr...@ucdavis.edu <mailto:dandr...@ucdavis.edu>
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