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How to tell your software which way round the data is. |
You must specify the orientation of your data by using the --orientation flag. What follows must be a string in the bg-space "initials" form, to describe the origin voxel.
When you work with a stack, the origin is the upper left corner when you show the first element stack[0, :, :] with matplotlib or when you open the stack with ImageJ. First dimension is the one that you are slicing, the second the height of the image, and the third the width of the image.
If the origin of your data (first, top left voxel) is the most anterior, superior, left part of the brain, then the orientation string would be "asl" (anterior, superior, left), and you would use:
--orientation asl
The order of the three initials must be the same as the axis order (sliced plane, height, width).