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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--
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: [EMAIL PROTECTED]
Web: http://home.uchicago.edu/~adick/
