Does anyone on this forum know AMIRA segmentation software? I have resliced/reoriented an anatomical image (.nii) in SPM. When I open the resulting image, it is nothing but a gray square without intensity values (NaN). Further, I want to register/reorient label fields made in on the original anatomical image in AMIRA so that they match the orientation of the resliced image. It appears to be possible to register the new anatomical orientation to the old label field orientation but not the old label field orientation to the new anatomical orientation. Does anyone have suggestions?
Apologies for a very late reply, but I’m quite familiar with Amira. It sounds like you did the rotation in SPM. If you are able to export the rotation information as degrees and translation as voxel units, you could apply the same transformation to your label data within Amira after importing. The data may import as a grayscale dataset and thus require a conversion to a label field to properly be connected. You’d then need to resample the transformed image in a way that does not cut off the data at the original image boundaries. Finally, if the datasets are the same dimensions, you can then relate/link the label data to the original image data that were resampled/resliced out of SPM. This will permit coinciding visuals and segmentation data for analysis.
If your institution has access to funding, you may consider upgrading your Amira installation. Amira 5 is pretty old, as it was updated to 6 in ~2016 and then to version 2019 and more recently 2020. This would give you access to their support line where questions like this could be answered much more quickly. New features are also being added, of course. You’re welcome to request a newest software trial and explain your question using this form: Amira Trial Request – Software Center