Documentation/Nightly/FAQ/Viewing and Resampling - Revision history

JChris.FillionR at 16:21, 15 July 2015

2015-07-15T16:21:07Z

JChris.FillionR at 17:33, 30 April 2014

2014-04-30T17:33:00Z

JChris.FillionR at 17:27, 30 April 2014

2014-04-30T17:27:16Z

Millerjv: /* How can I use the reformat widget view to resample my images? */

2013-06-25T12:50:25Z

How can I use the reformat widget view to resample my images?

Millerjv: /* How can I use the reformat widget view to resample my images? */

2013-06-25T12:49:21Z

How can I use the reformat widget view to resample my images?

Pieper: /* How can I use the reformat widget view to resample my images? */

2013-06-24T23:54:19Z

How can I use the reformat widget view to resample my images?

Pieper: /* How can I use the reformat widget view to resample my images? */

2013-06-24T21:01:57Z

How can I use the reformat widget view to resample my images?

Pieper: Created page with '='''User FAQ: {{{1}}}'''= ==What coordinate systems does Slicer use?== See this documentation of Slicer coordinate systems. ==How can I u…'

2013-06-24T21:01:39Z

Created page with '='''User FAQ: {{{1}}}'''= </includeonly> ==What coordinate systems does Slicer use?== See this documentation of Slicer coordinate systems. ==How can I u…'

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==What coordinate systems does Slicer use?==

See this [[Coordinate_systems|documentation of Slicer coordinate systems]].

==How can I use the reformat widget view to resample my images? ==

<code>
red = getNodes('vtkMRMLSliceNode*')['Red']
t = slicer.vtkMRMLLinearTransformNode()
t.SetAndObserveMatrixTransformToParent(red.GetSliceToRAS())
</code>

Then invert “t” and put my original volume under “t”.

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	See this [[Coordinate_systems\|documentation of Slicer coordinate systems]].		See this [[Coordinate_systems\|documentation of Slicer coordinate systems]].
		+
		+	== Is there a global coordinate system ? ==
		+
		+	There is no coordinate system in Slicer that is called Global. There is one called RAS. When you open Slicer, the middle of the pink wireframe box in the 3D view is at the origin of RAS. When a medical image is loaded in Slicer, it is oriented relative to the RAS coordinate system so the right hand of the patient is towards the R (first coordinate), the front of the patient is towards A (second coordinate). It's a right handed system.
		+
		+	To visualize "something", it is usually most convenient of to transform it to RAS, so it shows up relative to CT or MR images loaded in Slicer. When hovering the mouse over an image slice (2D), the RAS coordinates are displayed in the [[Documentation/{{documentation/version}}/Modules/DataProbe\|Data Probe]] located in lower left corner of the Slicer UI.
		+
		+	Source: http://slicer-devel.65872.n3.nabble.com/Reference-System-tp4031501p4031503.html

	==How can I use the reformat widget view to resample my images? ==		==How can I use the reformat widget view to resample my images? ==

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	='''User FAQ: {{{1}}}'''=		='''User FAQ: {{{1}}}'''=
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← Older revision		Revision as of 12:50, 25 June 2013
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	</pre>		</pre>

−	Then put your volume under ~~“t”~~.	+	Then put your volume under “t" or provide "t" as the transform to one of the Resample modules.

@@ Line 12: / Line 12: @@
 <pre>
 red = getNodes('vtkMRMLSliceNode*')['Red']
 t = slicer.vtkMRMLLinearTransformNode()
-t.SetAndObserveMatrixTransformToParent(red.GetSliceToRAS())
+t.SetAndObserveMatrixTransformToParent(m)
   </pre>
-Then invert “t” and put my original volume under “t”.  Note that it is probably better to copy the matrix rather than observing SliceToRAS directly.
+Then put your volume under “t”.

@@ Line 7: / Line 7: @@
 ==How can I use the reformat widget view to resample my images? ==
 <pre>
@@ Line 14: / Line 16: @@
   </pre>
-Then invert “t” and put my original volume under “t”.
+Then invert “t” and put my original volume under “t”.  Note that it is probably better to copy the matrix rather than observing SliceToRAS directly.