Hi Mahinda,

For question 1, if you use the new mris_preproc, as described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19821.html then yes, you are safe in computing the areas for each vertex. We have a recent paper that discuss current matters on pointwise area stuff, and that may answer your questions. Please, have a look here: http://www.sciencedirect.com/science/article/pii/S1053811912002996

All the best,

Anderson


On 02/05/12 02:02, Mahinda Yogarajah wrote:
Hi Doug,

Thanks for the swift answer to the earlier questions - can I clairfy some things:

1) Am I safe to use (and attempt to interpret) area/volume in a vertex wise analysis (as opposed to an ROI based analysis) using the basic concept you describe below - I have read on the forums about problems with regard to this - some have mentioned using "areal" instead area and others have mentioned the lack of "jacobian modulation' for volume calculations - what is the current thinking on these issues ...

2) With regard to visualisation of monte carlo simulation output - I made a mistake in my last post - when I visualise in qdec I highlight the mc-z file, and set the threshold to 1.3 which I believe is the default setting for the cluster wise p value - am I right in thinking that the threshold selected in the monte carlo box in qdec is the vertex-wise threshold ? I checked again when I click on find clusters and go to max and the table generated is slightly different to that output from the monte carlo run button as shown below - could you explain what the difference is ...

Thanks.

Mahinda

Output from Monte Carlo run:


ClusterNoMaxVtxMaxSize(mm^2)TalXTalYTalZCWPCWPLowCWPHiNVtxsAnnot

1-4.615105901851.87-20.7-20.357.40.005500.004600.006502195precentral

2-3.48264220584.30-40.445.5-10.60.047900.045200.05060942parsorbitalis

Output from Find clusters and go to max

============================================================

Generating cluster stats using min threshold of 1.3...

Found 2 clusters

Contrast: 'lh-Diff-Patient-Control-Cor-thickness-age', 15fwhm, DOF: 34

ClusterNoMaxVtxMaxSize(mm2)TalXTalYTalZ NVtxs Annotation

--------------------------------------- ----- ----------

1-2.259647851.87-22.0-29.552.2 2195precentral

2-1.319724584.30-38.150.0-3.4942rostralmiddlefrontal

============================================================




On 04/28/2012 09:45 PM, Mahinda Yogarajah wrote:
>  Dear Experts,
>
>  I had 2 questions with regard to vertex wise analysis using qdec.
>
>  1) How should one interpret the dependent variables area/pial area and
>  volume when comparing 2 groups with qdec and a vertex wise (as opposed
>  to ROI based) analysis - or are they uninterpretable in this context ?
>  I read briefly about areal as an alternative measure - could someone
>  explain the difference, and how thickness, volume and area related to
>  one another ?
volume = area * thickness. The "area" of a vertex is the average of the
triangles that surround it. For a group analysis, you can think of it as
drawing a small circle around a vertex in fsaverage space and asking how
big that circle is in each individual subject.
>
>  2) When running monte-carlo cluster wise multiple correction in qdec -
>  if one finds a significant cluster is it ok to view them within qdec
>  by highlighting the "mc-z ... " file in the analysis result box, and
>  then changing the minimum threshold to whatever value one selected for
>  the monte carlo simulation ?
No, the mc-z output has values equal to the cluster-wise p-value, so it
is not appropriate to apply the vertex-wise threshold.
>  The reason I ask is that the text ouput given by the monte carlo
>  cluster analysis gives different coorinates in the cluster table to
>  that output given when one clicks on the "find clusters and go to max"
>  button ...
Are you using the "abs" when you do the clustering? Is is possible that
it found a negative peak in the table but qdec goes to the positive peak?
>
>  Thanks.
>
>  Mahinda



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