Come to think of it, I would benefit from that utility, too.;-) Even
better would be an accurate, automated border drawing utility. Kidding
aside, we recognize this is a highly desirable enhancement, but pretty
tough to deliver right now.
John Harwell has added some caret_command features that can trim some of
the easy ones (e.g., calcarine posterior, central dorsal/medial):
SURFACE BORDER EXTREMA
caret_command -surface-border-extrema \
<input-topo-file> <input-coord-file> <input-border-file>
<border-name>
List the extrema for the surface, the extrema for the border, and the
difference between the extrema.
------------------------------------------------------------------------------
SURFACE BORDER NIBBLER (remove border points within a distance to
surface ext
rema)
caret_command -surface-border-nibbler \
<input-topo-file> <input-coord-file> <input-border-file>
<border-name>
<output-border-file> <surface-extrema-name-or-node-indicator>
<surface-extrema-offset-or-node-number> <pos-neg>
Remove points from the named border that are within that are on a .
specified side of a surface extrema or node number.
But your idea is kind of interesting.
Meanwhile, if you choose reference points which differ primarily along
the axis of interest, then the distance is a good proxy for the
component difference, so no math required. In either case, you'll be
surprised how fast you get good at guessing. Before long, you'll need
only a few tries, and it's always fun when your first guess is right. ;-)
On 11/30/2006 12:52 PM, Mateus Joffily wrote:
Hi Donna,
That's exactly what I did (although, there are some details in your
example that I didn't understand well, see below). But, instead of
keep going forth and back selecting nodes and subtracting their
coordinates values (I had to do it quite often), I was wondering if
there was not an utility that would automatically highlight all the
nodes that are at a given distance from my reference point. I am not
saying that it is a necessary utility, but, if it was already
implemented, I could benefit from it...
Thanks,
Mateus
For example, there's a pretty big x and z offset between this
occipital pole (first) and candidate most-posterior calcarine border
point:
In this example, I though that the biggest offset was for Y (dX:
15-28=-13; dY: -110 --78=32; dZ: -22 --6=-16). That's why you first
chose to adjust the Y distance, no?
Node 20734
Main Window Inflated XYZ: 15.015987396, -110.156700134, -22.251829147
Shape: -2.904558420 -2.124466896
Node 32819
Main Window Inflated XYZ: 27.664737701, -77.988800049,
-6.281192303 Distance: 38.076580048
Shape: -10.455765724 -8.209010124
So I compute -110 - -78 = 32 -- so this point is 32mm from the
occipital pole, so we need to find one whose y component of the
inflated coordinate is closer to like -110 + 24 = -86.
Hope this helps!
On 11/30/2006 06:53 AM, Mateus Joffily wrote:
Hi David,
Thanks for your reply. I asked for this capability because I am
trying to perform a spherical registration. Many landmarks are
defined as starting and terminating at a certain distance from an
anatomical reference point. I thought that a tool, which allows the
user to enter a reference point coordinate in the surface and,
after, displays every node that is at a given geodesic distance from
it, would be helpful
This capability is not essential for me. I was wondering if it was
already implemented in Caret.
Best regards,
Mateus
David Vanessen wrote:
Mateus,
First, it is important to clarify whether your request pertains to
nodes (as stated) or to foci. In Caret terminology, nodes refers
specifically to the points that make up a surface and have
locations specified within a coordinate file. Foci refers to
stereotaxically identified locations (typically fMRI activation
centers) that are specified within a foci file or foci projection
file. I'm guessing you are referring to foci, but let us know.
At present, I don't think that the capability you are asking about
exists for either nodes or foci. If you can let us know what you
will be using this for and whether this is a pressing need, it
will help us to prioritize the request. Also, if other Caret
users would like to see this functionality, let us know.
Best regards,
David
On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote:
If you were talking about geodesic distance (i.e., running along
the contour of the fiducial surface -- not as the crow flies
through the CSF/WM), then you could use the Surface: ROI feature
for this purpose. (First operation Geodesic Distance, and then
threshold the resulting metric at the desired distance.)
I'm not aware of something like that for 3D distances, but
there's a Make Sphere feature in Window: Script Builder. Worst
case, you could generate a sphere around the enclosing voxel and
map that ROI volume to the surface.
On 11/29/2006 11:18 AM, Mateus Joffily wrote:
Hi,
In Caret5.5, is there a way of selecting a node and finding all
(or some) nodes that are at a given distance from it? I think I
am looking for something similar to what is described in
section 2.17.2 (Foci Data Searches) of the 'Caret Tutorial – the
Basics'. But Section 2.17.2 regards only WebCaret. Does it exist
something similar to Caret5.5?
Thanks,
Mateus
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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see http://
home.att.net/~donna.hanlon for details.)
_______________________________________________
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_______________________________________________
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caret-users@brainvis.wustl.edu
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_______________________________________________
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caret-users@brainvis.wustl.edu
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_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see
http://home.att.net/~donna.hanlon for details.)
