I already started having fun with Caret! ;-) Thank you very much

Donna Dierker wrote:

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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