Hi Emma,

Please, see below:

On 13 October 2014 20:11, Emma Thompson <voneconomos@gmail.com> wrote:

Hi Anderson,
Thank you for your paper. I guess I am confused. I have analyzed my structural data with qdec, specifically looking at a measure of cortical thickness and volume. I'm considering looking at surface area as well but was told it wasn't a very good measure using qdec, I have no other information really. Could you speak to whether or not this measure is valid in so far as one runs it using qdec?

The data that is used in qdec comes from mris_preproc, which uses vertexwise interpolation with Jacobian correction for local stretches/shrinkages. The amount of area is preserved globally, which is desirable, although locally it's something difficult to achieve. If without any smoothing, the spatial correlation between mris_preproc and the method in the paper is about 0.65, and the correlation at a given vertex, across subjects, varies spatially. Note, however, that the smoothing -- that is applied by default -- should increase the correlation vastly, but I don't have the exact numbers at hand to provide yet.

For area, as well as for volume, the method shown in the paper is really the gold standard: it's pycnophylactic and thus guarantees that the amount of area is preserved locally everywhere in the brain during the interpolation. It's the same method used in GIS applications for geoprocessing. The downside is that the current implementation, using Matlab, is too slow (for the ico7, it can well take 10-15h per hemisphere in a single CPU).

Also, in your opinion, would it be redundant to look at surface area in addition to measures of cortical thickness and cortical volume?

Actually, the redundant bit here is volume. Area and thickness are uncorrelated phenotypically and genetically, and each provide different pieces of information (this is shown here and here). Volume is a mixture of both, in proportions that vary across the cortical mantle. I would not consider using volume given that thickness and area are available. Moreover, volume is also an "areal quantity" in the sense that it requires the same methods for interpolation as surface area itself, so all that is said above about area applies also to cortical volumes.

Hope this helps!

All the best,

Anderson

On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler <winkler@fmrib.ox.ac.uk> wrote:

Hi Donna,

In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmfit or qdec), without loss of areal quantities.

All the best,

Anderson

On 11 October 2014 04:05, Donna Dierker <donna@brainvis.wustl.edu> wrote:
Hi Emma,

I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here:

http://www.pnas.org/content/107/29/13135.figures-only

… which is similar, but not identical to the local gyrification index?

If so, would you use this measure on surfaces before or after registration to a target atlas?

Donna

On Oct 10, 2014, at 4:19 PM, Emma Thompson <voneconomos@gmail.com> wrote:

> Dear Freesurfers,
> I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks!

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