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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