On 05/01/2012 09:02 PM, Mahinda Yogarajah wrote:
Hi Doug,
Thanks for the swift answer to the earlier questions - can I clairfy some things:
- 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 ...
It is safe if you have the new version of mris_preproc.
- 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 ?
Yes
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 ...
Are you using "abs"? doug
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.
- 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.
- 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