[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:

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...


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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