Projects:SlicerFAQ:VoxelSizeFix - Revision history

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

2017-07-10T18:07:26Z

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

Meier at 16:21, 15 November 2010

2010-11-15T16:21:19Z

Meier: Created page with 'back to Slicer FAQ = How do I fix a wrong orientation of an image ? = '''Problem:''' My image appears upside down / flipped / facing the wrong way / I…'

2010-11-15T16:14:12Z

Created page with '*back to Slicer FAQ = How do I fix a wrong orientation of an image ? = *'''Problem:''' My image appears upside down / flipped / facing the wrong way / I…'

New page

*[[Projects:SlicerFAQ|back to Slicer FAQ]]

= 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

@@ Line 4: / Line 4: @@
 *'''Problem:''' My image appears distorted / stretched / with incorrect aspect ratio
 *'''Explanation:''' Slicer presents and interacts with images in ''physical'' space, which differs from the way the image is stored by a set of separate information that represents the physical "voxel size" and the direction/spatial orientation of the axes. If the voxel dimensions are incorrect or missing, the image will be displayed in a distorted fashion.  This information is stored in the image header. If the information is missing, a default of isotropic 1 x 1 x 1 mm size is assumed for the voxel.
-*'''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]. If you know the correct voxel size, enter it in the fields provided and hit RETURN after each entry. You should see the display update immediately. Ideally you should try to maintain the original image header information from the point of acquisition. Sometimes this information is lost in format conversion. Try an alternative converter or image format if you know that the voxel size is correctly stored in the original image. Alternatively you can try to edit the information in the image header, e.g. save the volume as (NRRD (.nhdr) format and open the ".nhdr" file with a text editor.
+*'''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]. If you know the correct voxel size, enter it in the fields provided and hit RETURN after each entry. You should see the display update immediately. Ideally you should try to maintain the original image header information from the point of acquisition. Sometimes this information is lost in format conversion. Try an alternative converter or image format if you know that the voxel size is correctly stored in the original image. Alternatively you can try to edit the information in the image header, e.g. save the volume as (NRRD (.nhdr) format and open the ".nhdr" file with a text editor.

@@ Line 1: / Line 1: @@
 *[[Projects:SlicerFAQ|back to Slicer FAQ]]
-= How do I fix a wrong orientation of an image ?  =
+= How do I fix incorrect voxel size / aspect ratio of a loaded image volume?  =
-*'''Problem:''' My image appears upside down / flipped / facing the wrong way / I have incorrect/missing axis orientation
+*'''Problem:''' My image appears distorted / stretched / with incorrect aspect ratio
-*'''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 set of separate information that represents the physical "voxel size" and the direction/spatial orientation of the axes. If the voxel dimensions are incorrect or missing, the image will be displayed in a distorted fashion.  This information is stored in the image header. If the information is missing, a default of isotropic 1 x 1 x 1 mm size is assumed for the voxel.
-*'''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
+*'''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]. If you know the correct voxel size, enter it in the fields provided and hit RETURN after each entry. You should see the display update immediately. Ideally you should try to maintain the original image header information from the point of acquisition. Sometimes this information is lost in format conversion. Try an alternative converter or image format if you know that the voxel size is correctly stored in the original image. Alternatively you can try to edit the information in the image header, e.g. save the volume as (NRRD (.nhdr) format and open the ".nhdr" file with a text editor.

Projects:SlicerFAQ:VoxelSizeFix - Revision history

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

Meier at 16:21, 15 November 2010

Meier: Created page with '*back to Slicer FAQ = How do I fix a wrong orientation of an image ? = *'''Problem:''' My image appears upside down / flipped / facing the wrong way / I…'

Meier: Created page with 'back to Slicer FAQ = How do I fix a wrong orientation of an image ? = '''Problem:''' My image appears upside down / flipped / facing the wrong way / I…'