On 08/16/2013 05:02 PM, Binod Thapa-Chhetry wrote:
> HI all,
>
> We had submitted a paper based on cortical thickness analysis in Qdec. 
> The reviewer's had couple concerns regarding the QDec analysis. We 
> would appreciate your help to address/resolve those issues. Here are 
> the concerns:
>
> (1) What was the rationale of using 10mm smoothing? The typical fMRI 
> values for volumteric work is 2-3 x the original voxel size. What's 
> the reason for this value?
>
> Our response so far: A smoothing kernel of 10 mm was chosen because 
> this setting had been published recently in articles that performed 
> similar analyses.  10 mm therefore was a typical parameter for this 
> type of analysis.  This setting was also the default in the QDEC GUI, 
> also suggesting that it was a typical setting.  We only performed 
> analyses of the data for this project using this setting and did not 
> iteratively test multiple kernel widths.  Also, the FWHM for cortical 
> thickness analyses is somewhat larger than that used in fMRI analyses 
> because it is applied to surface, as opposed to volume-based data.  
> Surface based data are not prone to the same artifacts of including 
> white matter, csf or brain tissue on the other side of a sulcus as 
> volume-based data are.
I think this is a good answer for a question that is not entirely fair. 
Aside from a few arguments about making GRF work, no one has ever had 
much of a justification for the particular choice of FWHM. It is just 
traditional at this point. You might point out that more smoothing is 
generally considered worse and that 10mm on the surface is much less 
than 10mm in the volume and people use 10mm in the volume is not unusual.
>
> (2) What's the p-value to get in for a cluster-wise analysis and what 
> size is a significant cluster? It's important to know these non 
> cluster-wise values to get a sense of the parameters that determine 
> significance.
>
> Our response so far: QDEC does not have a parameter that can be 
> adjusted for cluster size or extent as other whole brain analyses such 
> as Statistical Parametric Mapping do.  The researcher can only 
> indicate a statistical cutoff.  We used a p value cutoff of 0.05 after 
> a correction for multiple comparisons that was based on the Monte 
> Carlo permutation cluster analysis with 10,000 iterations. 
> Additionally, our findings comprise of pretty large clusters. This 
> obviates the reason for cluster-thresholding  based on size.
I'm not sure what the reviewer is asking. Is he/she asking for the 
cluster-forming, ie, voxel-wise, threshold? Or the p-value threshold for 
the cluster that you used to report clusters? You should report both. 
Both can be set in the QDEC GUI. I think the defaults are .01 and .05 
respectively. Given the clusterwise p-value, there is a corresponding 
critical cluster size. You can get this from a file in the QDEC output 
folder (in the contrast subfolder). The file will be called something 
like "cache.th20.abs.pdf.dat". The 2nd column gives you the cluster size 
(in mm2) and the 4th column gives you the clusterwise p-value. Find the 
size of the cluster that corresponds to .05. In one data set I looked 
at, the size was about 328mm^2

doug



>
>
> Thanks in advance for the response.
> Binod
>
>
>
>
>
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