| My data is in axial slices that require the following flips to bring them
| into radiological orientation:
| sagittal images must be flipped horizontally
| axial images must be flipped vertically.
Depending how you view the sagittal and axial images, then these could
both refer to the same flip, which would mean a flip in the anterior-posterior
direction.
| I perform these flips in stimulate software before converting to analyze
| file format. When I display these axial slices in spm, the sagittal and
| coronal reconstructions are upside down.
| In an attempt to correct this, I changed the affine norm etimates during
| spatial normalization to -1, -1, -1. However, when I try to display these
| images, I get a blank display window. How can I check the images to
| determine whether they are in the proper orientation? Is this the correct
| fix?
It is probably easier to reorient the images via the <Display> button before
spatially normalising. Try various translations and rotations, such that
the crosshairs lie somewhere near the AC, and the images are in the same
orientations as those that are distributed with SPM (in templates, canonical
or apriori subdirectories). If you are using the default affine starting
estimates, then the subjects left should appear on the right of the
transverse image.
Once you have worked out the approximately correct orientation, then you
can save the new position for all the images that are aligned with the
image that is being displayed, by clicking the <Reorient images..> button
and selecting the appropriate files.
All the best,
-John
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