[caret-users] listing clusters

[David Van Essen]

Christa-Lynn,

Two comments.

1) Working from the menu options, you can use the Surface: Region of  
Interest window to do something that I think is close to what you want.

Select your overall ROI.  If, for example, you want everything except  
the medial wall, choose
Selection Method: Nodes with Paint;
Category: Medial Wall;
Select Name: Medial Wall;
Select Nodes
Invert Node Selection.

Then, with the metric file copied to have a *.surface shape file  
ending, load it as a surface shape file and view the relevant column  
in the main window surface.

Select Surface ROI: Operate on Selected Nodes: Operation: Surface  
Shape Cluster Analysis, and set the threshold where desired.

The Report column will show the surface area and the center of gravity  
of each cluster.

You said that you really want the maximum value of each cluster and  
the coordinates of that maximum.  I'm not aware of a Caret function  
that does that. However, the request is a reasonable one, and if it is  
indeed what you want we can add it to John Harwell's to-do list  
(presumably better to operate on metric files directly).  One  
important issue would be what to do about ties - it will not be  
uncommon for multiple nodes within a cluster to have the 'maximum'  
value.  If so, should all of them be reported?  (could be a long  
list)  Or should the COG of all 'peak nodes' within a cluster be  
reported?  Or some other sensible strategy?

It would help to get feedback on this issue and also whether other  
Caret users would find this to be a useful analysis function.

2) A separate matter is that whenever I encounter someone still using  
our 'old' Colin atlas, I take the opportunity to recommend strongly  
that you switch to the new PALS human atlas, which we consider to be  
superior on many grounds.  For the background and rationale, see:

Van Essen & Dierker, Surface-based and probabilistic atlases of  
primate cerebral cortex. Neuron. 2007;56:209-25
http://www.ncbi.nlm.nih.gov/pubmed/17964241

and/or:
Van Essen A Population-Average, Landmark- and Surface-based (PALS)  
atlas of human cerebral cortex.
Neuroimage. 2005  28:635-62
http://www.ncbi.nlm.nih.gov/pubmed/16226584

For the atlas dataset and tutorial, see
http://sumsdb.wustl.edu/sums/directory.do?id=6585200&dir_name=CARET_TUTORIAL_SEPT-06

Good luck!

David VE


On Jan 10, 2008, at 6:27 PM, donovan at psych.ucsb.edu wrote:

> Hi,
> I have a question on how to get a list of clusters from a  
> thresholded metric file. I am displaying SPM2 t images (fMRI) onto  
> the human.colin.Cerebral atlas in Caret v5.3. I am able to threshold  
> the image but I can't seem to figure out how to get a list of maxima  
> and their coordinates. I found in your archives a suggestion to copy  
> the metric file to a surface_shape but I am unfamiliar with the  
> command line prompts you suggested (I have only used the menus).   
> Any help you can give me with doing this through the menus would be  
> greatly appreciated.
>
> Thanks in advance!
>
> Christa-Lynn Donovan
> PhD Candidate
> Department of Psychology
> University of California
> Santa Barbara, 93106
>
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://pulvinar.wustl.edu/mailman/listinfo/caret-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://brainvis.wustl.edu/pipermail/caret-users/attachments/20080110/265a5822/attachment.html