Coordinate systems - Revision history

JChris.FillionR at 14:48, 26 July 2023

2023-07-26T14:48:38Z

2021-10-29T01:50:18Z

Fixed link to coordinate systems demystified ppt

2014-06-30T14:00:15Z

References

2014-02-12T14:33:20Z

Introduction

2014-02-12T14:33:03Z

Introduction

2014-02-12T14:32:16Z

Introduction

2013-08-02T15:06:15Z

Introduction

2013-05-14T16:40:14Z

Relations to other software / conventions

2013-05-14T16:39:45Z

2011-02-06T19:51:22Z

References

← Older revision		Revision as of 14:48, 26 July 2023
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		+	{{documentation/banner\|text=[https://slicer.readthedocs.io/en/latest/user_guide/coordinate_systems.html For the latest version of this page, visit the read-the-docs.]}}
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	=Introduction=		=Introduction=
	One of the issues while dealing with medical images and applications are the differences between the coordinate systems. There are three coordinate systems commonly used in imaging applications: a difference can be made between the '''world''', '''anatomical''' and the '''image coordinate system'''.		One of the issues while dealing with medical images and applications are the differences between the coordinate systems. There are three coordinate systems commonly used in imaging applications: a difference can be made between the '''world''', '''anatomical''' and the '''image coordinate system'''.

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 Anatomy image based on [http://www.my-ms.org/mri_plane_math.htm image shared by the My MS organization].
-Note that Chand John of Stanford created a [http://www.na-mic.org/Wiki/images/3/3f/Coordinate_Systems_Demystified.ppt detailed powerpoint presentation about the way coordinates are handled in Slicer].
+Note that Chand John of Stanford created a [https://www.na-mic.org/w/img_auth.php/3/3f/Coordinate_Systems_Demystified.ppt detailed powerpoint presentation about the way coordinates are handled in Slicer].
 ==World coordinate system==

← Older revision		Revision as of 14:00, 30 June 2014
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	* http://nifti.nimh.nih.gov/nifti-1/documentation/faq		* http://nifti.nimh.nih.gov/nifti-1/documentation/faq
	* http://teem.sourceforge.net/nrrd/format.html		* http://teem.sourceforge.net/nrrd/format.html
		+	* [http://medical.nema.org/dicom/2013/output/chtml/part03/sect_C.7.html#sect_C.7.6.2.1.1 DICOM 2013 PS3.3 Image Position and Image Orientation]

@@ Line 10: / Line 10: @@
 Anatomy image based on [http://www.my-ms.org/mri_plane_math.htm image shared by the My MS organization].
-Note that Chand John of Stanford created a [http://www.na-mic.org/Wiki/images/3/3f/Coordinate_Systems_Demystified.ppt |detailed powerpoint presentation about the way coordinates are handled in Slicer].
+Note that Chand John of Stanford created a [http://www.na-mic.org/Wiki/images/3/3f/Coordinate_Systems_Demystified.ppt detailed powerpoint presentation about the way coordinates are handled in Slicer].
 ==World coordinate system==

@@ Line 10: / Line 10: @@
 Anatomy image based on [http://www.my-ms.org/mri_plane_math.htm image shared by the My MS organization].
-Note that Chand John of Stanford created a [[File:Coordinate Systems Demystified.ppt‎ |detailed powerpoint presentation about the way coordinates are handled in Slicer]].
+Note that Chand John of Stanford created a [http://www.na-mic.org/Wiki/images/3/3f/Coordinate_Systems_Demystified.ppt |detailed powerpoint presentation about the way coordinates are handled in Slicer].
 ==World coordinate system==

← Older revision		Revision as of 14:32, 12 February 2014
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	Anatomy image based on [http://www.my-ms.org/mri_plane_math.htm image shared by the My MS organization].		Anatomy image based on [http://www.my-ms.org/mri_plane_math.htm image shared by the My MS organization].
		+
		+	Note that Chand John of Stanford created a [[File:Coordinate Systems Demystified.ppt‎ \|detailed powerpoint presentation about the way coordinates are handled in Slicer]].

	==World coordinate system==		==World coordinate system==

← Older revision		Revision as of 15:06, 2 August 2013
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	Each coordinate system serves one purpose and represents their data in different ways.		Each coordinate system serves one purpose and represents their data in different ways.
		+
		+	Anatomy image based on [http://www.my-ms.org/mri_plane_math.htm image shared by the My MS organization].

	==World coordinate system==		==World coordinate system==

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 * The right axis is flipped, so the first column of the '''IJtoRS'''-matrix has just an inverted sign
-== Relations to other software / conventions ==
+= Relations to other software / conventions =
-=== Using MATLAB to map Slicer RAS coordinates (e.g. fiducials) to voxel space of a NIfTI Image ===
+== Using MATLAB to map Slicer RAS coordinates (e.g. fiducials) to voxel space of a NIfTI Image ==
 To extract the "voxel to world" transformation matrix from the NIFTI file's header (entry: qto_xyz:1-4 ) in Matlab:

← Older revision		Revision as of 19:51, 6 February 2011
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	=References=		=References=
−	* ...	+	* http://people.cs.uchicago.edu/~glk/unlinked/nrrd-iomf.pdf
		+	* http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm
		+	* http://nifti.nimh.nih.gov/nifti-1/documentation/faq
		+	* http://teem.sourceforge.net/nrrd/format.html