[caret-users] Extent threshold

[Anthony Steven Dick]

Hi Kevin-

We use permutation methods outlined in some recent papers from Nichols 
and Hayasaka (e.g., see Nichols & Holmes, 2001; HBM 15, 1-25) to 
determine minimum cluster sizes.

As Donna suggested, the AFNI/SUMA SurfClust command is ideal for this. 
We use it in combination with R statistical package, and it gives quite 
good results. The only downside is it takes some time to run the 
permutations unless you have access to a grid computing system.

Anthony

Donna Dierker wrote:
> Hi Kevin,
>
> Not directly, as far as I know. The closest two such features are these:
>
> * When you multi-fiducial map a fMRI volume onto the PALS_B12 atlas, 
> you can specify a threshold. Then it maps the volume to each of the 12 
> PALS_B12 hemispheres, and calculates the suprathreshold area of each 
> hemisphere. Then it computes an average area and generates a threshold 
> that limits the MFM extent to that area.
>
> * After mapping your functional volume onto the surface and saving as 
> a metric file (node:scalar pair), then you can open the metric file as 
> a surface shape file and use Surface: ROI to do a cluster report on 
> the metric file. I haven't tried it using 0.0 as a threshold, but it's 
> probably possible to do so. Caret will then find all the clusters over 
> that threshold. Save the output of that file; trim the header info; 
> and sort on column 5 (corrected size). (If you're using a single 
> individual's surface, rather than an average surface, then cols 4 and 
> 5 will be identical, and you won't need a distortion metric file; for 
> average surfaces, you need a metric like our PALS distortion metrics 
> that pump up the area in regions of high variability (e.g., IPS), that 
> get smoothed out during averaging.)
>
> I'm not aware of any more direct methods; you might try the AFNI list; 
> Ziad Saad may have something like that for SUMA.
>
> Donna
>
> On 08/07/2007 09:22 AM, Kevin Guise wrote:
>> Greetings
>>
>> I've searched through previous postings and the caret documentation 
>> but I am
>> unable to find any information regarding a method to set a minimum 
>> cluster
>> extent threshold while projecting functional activation onto a 
>> surface map.
>> Is this at all implemented in caret, or can anyone suggest an equivalent
>> method?
>>
>> Best
>> Kevin
>>
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>
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-- 
Anthony Steven Dick, Ph.D.
Post-Doctoral Scholar
Human Neuroscience Laboratory
Department of Neurology
The University of Chicago
5841 S. Maryland Ave. MC-2030
Chicago, IL 60637
Phone: (773)-834-7770
Email: adick at uchicago.edu
Web: http://home.uchicago.edu/~adick/