[slicer-users] Transform slicer fiducials coordinates to scanner-space coordinates

Isaiah Norton isaiah.norton at gmail.com
Wed Aug 3 21:50:22 EDT 2011


Please see this discussion for details of the coordinates:
http://www.slicer.org/slicerWiki/index.php/Coordinate_systems

With the centered option, the origin is set for each axis as 1/2 *
dimension_pixels * spacing. There are also potentially sign changes (usually
in the Z axis) depending on the axis origin per above, and the tags
mentioned below.

x_0 = x_dim * x_spacing * .5
y_0 = y_dim * y_spacing * .5
z_0 = z_dim * z_spacing *.5

To get scanner space you need at least the DICOM tags "Image Position
Patient" and "Image Orientation Patient". You can get the tag values in the
Slicer "load volume" view, but I don't know if there is an automatic way to
get a Slicer-usable transform. Note: Slicer respects those tags when loading
images, so if you load without checking 'centered' then coordinates will be
correct relative to scanner space.

Hope this helps to get started...

-Isaiah



On Wed, Aug 3, 2011 at 10:58 AM, Gabriele Arnulfo <tartuz at gmail.com> wrote:

> Dear Slicer experts,
>
> I'm facing an annoying problem I cannot understand how to transform some
> fiducial-points from slicer-compliant coordinate space to the original
> scanner space.
>
> I've already looked inside the documentation searching for some tips and
> explanation but I had no luck at all. (also google didn't help much)
>
> I need the transformation matrix that is applied to the volume, during
> the loading phase, when the "centered" option has been chosen. I cannot
> simply use the 3DSlicer interface and manually check each points.
>
> Any suggestion/tips are appreciated.
>
> Thank in advance,
>
> gabriele
>
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