Boundary Coordniates

[Andrea Jackowski]

Hi Xenios

Can BioImage output boundary coordinates for a brain structure, let´s say the corpus callosum in a mid-sagittal slice?

Thanks in advance

Andrea

[Xenios Papademetris]

Probably .. what's the input .... i.e. how are you tracing/painting the structure?

Xenios

[Andrea Jackowski]

Xenios
The input is a cropped midsagittal slice with the corpus callosum thresholded and edited. I usually get these coordinates in analyze.
Thanks!
aj

[Xenios Papademetris]

Andrea,

To clarify -- this is effectively an objectmap, i.e. a binary image with one inside and zero outside.

Xenios

[Andrea Jackowski]

Hi Xenios

Yes, it is a binary object.

Thanks

Andrea

[Xenios Papademetris]

The easiest way is to simply extract the iso-contour using the surface control (see
 http://bioimagesuite.org/doc/node15.html#SECTION03630000000000000000)

1. (optionally) Threshold the image to make sure it is 0 .. 100  ( as opposed to 0 .. 1) , this will help things
2  Under Surface Control/Tools extract iso-contour with level=50 (or 0.5 if you did not threshold), then save the resulting surface as a text file (File/Save in the surface control)

The first part of the resulting text file are the points (x,y,z,x,y,z ...)

Xenios