[EMAIL PROTECTED] wrote:
Dear FreeSurfer Gurus
I have two questions about surfcluster that I would appreciate some
help with....
1. What 'connectivity radius' is used in surfcluster? It seems to be
hardwired, because I can't find a flag to specify it. By connectivity
radius I do not mean the minimum cluster size that of course can be
specified, but the minimum distance in mm that two vertexes can be
within in order to be considered part of the same cluster on the
surface. If this value is low, then clusters are probably defined as
cases of adjacent vertexes (perhaps within 1 edge distance?), but I
could see uses for changing this parameter so that 'adjacency' would
be defined somewhat more liberally (especially in cases when smoothing
is low).
SUMA's surfclust has the -rad option that achieves this (["Maximum
distance between an activated node and the cluster to which it
belongs.Distance is measured on the surface's graph (mesh)"] and I was
wondering if FreeSurfer has this option. If not, does anyone know
what the hard coded value is? Knowing it will help choosing smoothing
parameters on the surface.
Two vertices must share a vertex to be considered in the same cluster.
2. When seeing the textual results of surfcluster, it is indeed very
useful to see the Max T, cluster size and number of nodes in cluster.
But, for purposes of some permutation algorithms, it would be
extremely useful to be able to know the mean T value in each cluster.
This enables calculating the *mass* of each cluster, defined roughly
as the number of vertexes multiplied by the mean T value (Bullmore,
1999). This lets one normalize for T values, and define 'reliable'
clusters are those that pass a certain mass, independent of their
size.. Would it be possible to get the mean T value in each cluster as
an output from surfcluster?
Obviously one could script a utility that for each cluster, computes
its mean T by cross referencing the cluster-tagged output with the T
value of each vertex (pivot table by cluster), BUT, getting the mean
cluster T directly from surfcluster would be a great feature.
Currently, this is not an option, but I'll consider it for future
implementation.
doug
Thank you for your time and patience,
Best,
Uri
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Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
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