Dear Experts, <br><br>I have some related questions:<br><br>1) Am I right in thinking that the default settings for recon-all produce aparc files where the areas are based on white matter and not pia ?<br>2) Therefore am I right in assuming that when I use aparcstats2table across my subjects using &quot;--meas area&quot;, the area is also going to be based on white matter unless I redo the processing using mris_anatomical with a &quot;pial&quot; flag<br>
3) If the above is correct, why is the default to measure areas based on white matter - intuitively this does not make sense to me or seem as useful as gray matter ROI areas (particularly as from my understanding there are further assumptions made in the algorithsm that does the labelling of underlying white matter from the cortex) - are their papers where white matter areas are being reportted ?<br>
4) In a vertex wise analysis of area (using newer version of mris_preproc) what nuisance factors are people using - does it make sense to use total brain surface area (rather than say ICV as one might use in thickness) and in which case does it make a difference to use total pial or white matter area ?<br>
5) Finally what do the dependent measures - intensity_deep/intensity_superficial,  intensity_deep.mgz/intensity_superficial.mgz and white K/H measure in qdec ...<br><br>Thanks.<br><br>Mahinda<br><br>