Projects:SlicerFAQ:ImageOrientationFix - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:40:43Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Meier: /* How do I fix a wrong orientation of an image ? */

2010-11-11T17:07:42Z

How do I fix a wrong orientation of an image ?

Meier at 17:06, 11 November 2010

2010-11-11T17:06:50Z

Meier at 17:06, 11 November 2010

2010-11-11T17:06:16Z

Meier at 16:48, 11 November 2010

2010-11-11T16:48:28Z

Meier at 16:42, 11 November 2010

2010-11-11T16:42:40Z

Meier at 16:42, 11 November 2010

2010-11-11T16:42:26Z

Meier: Created page with 'back to Slicer FAQ = How do I fix an wrong orientation of a loaded image volume? = My image appears upside down / facing the wrong way / I have incorrect/missing axis or…'

2010-11-11T16:39:12Z

Created page with '*back to Slicer FAQ = How do I fix an wrong orientation of a loaded image volume? = *My image appears upside down / facing the wrong way / I have incorrect/missing axis or…'

New page

*[[back to Slicer FAQ]]

= How do I fix an wrong orientation of a loaded image volume? =
*My image appears upside down / facing the wrong way / I have incorrect/missing axis orientation

*Slicer presents and interacts with images in '''physical'' space, which differs from the way the image is stored by a separate ''transform'' that defines how large the voxels are and how the image is oriented in space, e.g. which side is left or right. This information is stored in the image header, and different image file formats have different ways of storing this information. If Slicer supports the image format, it should read the information in the header and display the image correctly. If the image appears upside down or with distorted aspect ratio etc, then the image header information is either missing or incorrect.
*You can correct the voxel dimensions and the image origin in the Info tab of the [http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes module], and you can reorient images via the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module]. Reorientation however will work only if the incorrect orientation involves rotation or translation. If axes are flipped (e.g. if left & right are flipped because the x-axis direction is defined incorrectly), then there is no tool in Slicer to alter that. This is by design; Slicer does not want to offer tools to (inadvertedly) manipulate image information that should be static and could lead to misrepresented image data.
*However fixing incorrect orientations such as flipped axes is not that hard and can be done with the help of Slicer:
:1. load the image into slicer (Load Volume, Add Data,Load Scene..)
:2. save the image back out as ''NRRD (.nhdr)'' format.
:3. open the ''.nhdr'' with a text editor of your choice. You should see a line that looks like this:
space: left-posterior-superior
sizes: 448 448 128
space directions: (0.5,0,0) (0,0.5,0) (0,0,0.8)
:4. the three brackets ( ) represent the coordinate axes as defined in the ''space'' line above, i.e. the first one is left-right, the second anterior-posterior, and the last inferior-superior. To flip an axis place a minus sign in front of the respective number, which is the voxel dimension. E.g. to flip left-right, change the line to
space directions: ('''-'''0.5,0,0) (0,0.5,0) (0,0,0.8)
:5. alternatively if the entire orientation is wrong, i.e. coronal slices appear in the axial view etc., you may easier just change the ''space'' field to the proper orientation. Note that Slicer uses ''RAS'' space by default, i.e. first (x) axis = left-'''r'''ight, second (y) axis = posterior-'''a'''nterior, third (z) axis = inferior-'''s'''uperior
:6. save & close the edited ''.nhdr'' file and reload the image in slicer to see if the orientation is now correct.

@@ Line 4: / Line 4: @@
 *'''Problem:''' My image appears upside down / flipped / facing the wrong way / I have incorrect/missing axis orientation
 *'''Explanation:''' Slicer presents and interacts with images in ''physical'' space, which differs from the way the image is stored by a separate ''transform'' that defines how large the voxels are and how the image is oriented in space, e.g. which side is left or right.  This information is stored in the image header, and different image file formats have different ways of storing this information. If Slicer supports the image format, it should read the information in the header and display the image correctly. If the image appears upside down or with distorted aspect ratio etc, then the image header information is either missing or incorrect.
-*'''Fix:''' You can correct the voxel dimensions and the image origin in the Info tab of the [http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes module], and you can reorient images via the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module]. Reorientation however will work only if the incorrect orientation involves rotation or translation. If axes are flipped (e.g. if left & right are flipped because the x-axis direction is defined incorrectly), then there is no tool in Slicer to alter that. This is by design; Slicer does not want to offer tools to (inadvertedly) manipulate image information that should be static and could lead to misrepresented image data.
+*'''Fix:''' You can correct the voxel dimensions and the image origin in the Info tab of the [https://www.slicer.org/wiki/Modules:Volumes-Documentation-3.6 Volumes module], and you can reorient images via the [https://www.slicer.org/wiki/Modules:Transforms-Documentation-3.6 Transforms module]. Reorientation however will work only if the incorrect orientation involves rotation or translation. If axes are flipped (e.g. if left & right are flipped because the x-axis direction is defined incorrectly), then there is no tool in Slicer to alter that. This is by design; Slicer does not want to offer tools to (inadvertedly) manipulate image information that should be static and could lead to misrepresented image data.
 *However fixing incorrect orientations such as flipped axes is not that hard and can be done with the help of Slicer:
 :1. load the image into slicer (Load Volume, Add Data,Load Scene..)

@@ Line 3: / Line 3: @@
 = How do I fix a wrong orientation of an image ?  =
 *'''Problem:''' My image appears upside down / flipped / facing the wrong way / I have incorrect/missing axis orientation
-*'''Explanation:''' Slicer presents and interacts with images in '''physical'' space, which differs from the way the image is stored by a separate ''transform'' that defines how large the voxels are and how the image is oriented in space, e.g. which side is left or right.  This information is stored in the image header, and different image file formats have different ways of storing this information. If Slicer supports the image format, it should read the information in the header and display the image correctly. If the image appears upside down or with distorted aspect ratio etc, then the image header information is either missing or incorrect.
+*'''Explanation:''' Slicer presents and interacts with images in ''physical'' space, which differs from the way the image is stored by a separate ''transform'' that defines how large the voxels are and how the image is oriented in space, e.g. which side is left or right.  This information is stored in the image header, and different image file formats have different ways of storing this information. If Slicer supports the image format, it should read the information in the header and display the image correctly. If the image appears upside down or with distorted aspect ratio etc, then the image header information is either missing or incorrect.
 *'''Fix:''' You can correct the voxel dimensions and the image origin in the Info tab of the [http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes module], and you can reorient images via the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module]. Reorientation however will work only if the incorrect orientation involves rotation or translation. If axes are flipped (e.g. if left & right are flipped because the x-axis direction is defined incorrectly), then there is no tool in Slicer to alter that. This is by design; Slicer does not want to offer tools to (inadvertedly) manipulate image information that should be static and could lead to misrepresented image data.
 *However fixing incorrect orientations such as flipped axes is not that hard and can be done with the help of Slicer:

@@ Line 3: / Line 3: @@
 = How do I fix a wrong orientation of an image ?  =
 *'''Problem:''' My image appears upside down / flipped / facing the wrong way / I have incorrect/missing axis orientation
 *'''Explanation:''' Slicer presents and interacts with images in '''physical'' space, which differs from the way the image is stored by a separate ''transform'' that defines how large the voxels are and how the image is oriented in space, e.g. which side is left or right.  This information is stored in the image header, and different image file formats have different ways of storing this information. If Slicer supports the image format, it should read the information in the header and display the image correctly. If the image appears upside down or with distorted aspect ratio etc, then the image header information is either missing or incorrect.
 *'''Fix:''' You can correct the voxel dimensions and the image origin in the Info tab of the [http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes module], and you can reorient images via the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module]. Reorientation however will work only if the incorrect orientation involves rotation or translation. If axes are flipped (e.g. if left & right are flipped because the x-axis direction is defined incorrectly), then there is no tool in Slicer to alter that. This is by design; Slicer does not want to offer tools to (inadvertedly) manipulate image information that should be static and could lead to misrepresented image data.

@@ Line 2: / Line 2: @@
 = How do I fix a wrong orientation of an image ?  =
-*My image appears upside down / flipped / facing the wrong way / I have incorrect/missing axis orientation
+*'''Problem:''' My image appears upside down / flipped / facing the wrong way / I have incorrect/missing axis orientation
-*Slicer presents and interacts with images in '''physical'' space, which differs from the way the image is stored by a separate ''transform'' that defines how large the voxels are and how the image is oriented in space, e.g. which side is left or right.  This information is stored in the image header, and different image file formats have different ways of storing this information. If Slicer supports the image format, it should read the information in the header and display the image correctly. If the image appears upside down or with distorted aspect ratio etc, then the image header information is either missing or incorrect.
+*'''Explanation:''' Slicer presents and interacts with images in '''physical'' space, which differs from the way the image is stored by a separate ''transform'' that defines how large the voxels are and how the image is oriented in space, e.g. which side is left or right.  This information is stored in the image header, and different image file formats have different ways of storing this information. If Slicer supports the image format, it should read the information in the header and display the image correctly. If the image appears upside down or with distorted aspect ratio etc, then the image header information is either missing or incorrect.
-*You can correct the voxel dimensions and the image origin in the Info tab of the [http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes module], and you can reorient images via the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module]. Reorientation however will work only if the incorrect orientation involves rotation or translation. If axes are flipped (e.g. if left & right are flipped because the x-axis direction is defined incorrectly), then there is no tool in Slicer to alter that. This is by design; Slicer does not want to offer tools to (inadvertedly) manipulate image information that should be static and could lead to misrepresented image data.
+*'''Fix:''' You can correct the voxel dimensions and the image origin in the Info tab of the [http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes module], and you can reorient images via the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 Transforms module]. Reorientation however will work only if the incorrect orientation involves rotation or translation. If axes are flipped (e.g. if left & right are flipped because the x-axis direction is defined incorrectly), then there is no tool in Slicer to alter that. This is by design; Slicer does not want to offer tools to (inadvertedly) manipulate image information that should be static and could lead to misrepresented image data.
 *However fixing incorrect orientations such as flipped axes is not that hard and can be done with the help of Slicer:
 :1. load the image into slicer (Load Volume, Add Data,Load Scene..)

@@ Line 1: / Line 1: @@
 *[[Projects:SlicerFAQ|back to Slicer FAQ]]
-= How do I fix an wrong orientation of a loaded image volume?  =
+= How do I fix a wrong orientation of an image ?  =
-*My image appears upside down / facing the wrong way / I have incorrect/missing axis orientation
+*My image appears upside down / flipped / facing the wrong way / I have incorrect/missing axis orientation
 *Slicer presents and interacts with images in '''physical'' space, which differs from the way the image is stored by a separate ''transform'' that defines how large the voxels are and how the image is oriented in space, e.g. which side is left or right.  This information is stored in the image header, and different image file formats have different ways of storing this information. If Slicer supports the image format, it should read the information in the header and display the image correctly. If the image appears upside down or with distorted aspect ratio etc, then the image header information is either missing or incorrect.

← Older revision		Revision as of 16:42, 11 November 2010
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−	*[[Projects:SlicerFAQ back to Slicer FAQ]]	+	*[[Projects:SlicerFAQ\|back to Slicer FAQ]]

	= How do I fix an wrong orientation of a loaded image volume? =		= How do I fix an wrong orientation of a loaded image volume? =

Projects:SlicerFAQ:ImageOrientationFix - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Meier: /* How do I fix a wrong orientation of an image ? */

Meier at 17:06, 11 November 2010

Meier at 17:06, 11 November 2010

Meier at 16:48, 11 November 2010

Meier at 16:42, 11 November 2010

Meier at 16:42, 11 November 2010

Meier: Created page with '*back to Slicer FAQ = How do I fix an wrong orientation of a loaded image volume? = *My image appears upside down / facing the wrong way / I have incorrect/missing axis or…'

Meier: Created page with 'back to Slicer FAQ = How do I fix an wrong orientation of a loaded image volume? = My image appears upside down / facing the wrong way / I have incorrect/missing axis or…'