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, [EMAIL PROTECTED] 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@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
