- If image is way off the center of the Field of View
The above can be rectified by using the Interactive Centering and Rotation
module to move the image approximately the center of the field of view.
You can find this module in
Toolbox --> Transformation -->Spatial 3D
- If you have deskulled your image
The SPM spatial normalization algorithm expects that the skull is available
on your image. Therefore it would be a good idea not to de-skull the
brain prior to running it through the Spatial Normalization module.
-
If you have defined too many non-linear iterations
Setting too many non-linear iterations results in undesired warping
of the brain at times. Usually a value of around 2 to 3 for the non-linear
iterations appears to work well.
- If your voxel dimensions are wrong
Wrong voxel dimensions can cause strange results with your data.
Go to Image Properties and check on the same and rectify it if the
dimensions are wrong. Looking at the image in the ortho viewer could
also give you a visual warning that your voxel dimensions are wrong
(your brain might look squished).
- Origin is set poorly
Make sure you set the origin close to the Anterior Commissure. Poor
definition of the origin could cause problems for spatial normalization.
- You do not have enough coverage of the brain
To rectify this you could manually edit the template (found in $PXHOME/images/SPM/templates)
and then open this template into MEDx. You will then need to use this
edited template as your User Defined Template and perform the spatial
normalization.
- Extremely noisy data
You could threshold your image to remove as much noise as possible
and use this as the Derive From Volume. You could then apply the derived
parameters to the original images(s).
If you have a question that you would like to see addressed in our list
of Frequently Asked Questions, please contact
customer support.
