[caret-users] Extent threshold

[Donna Dierker]

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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