Difference between revisions of "Projects:SlicerFAQ:VoxelSizeFix"
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(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…') |
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| − | = How do I fix a | + | = How do I fix incorrect voxel size / aspect ratio of a loaded image volume? = |
| − | *'''Problem:''' My image appears | + | *'''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 | + | *'''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 | + | *'''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. |
Revision as of 16:21, 15 November 2010
Home < Projects:SlicerFAQ:VoxelSizeFixHow do I fix incorrect voxel size / aspect ratio of a loaded image volume?
- 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 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.
