11/22/2023 0 Comments Metaimage volumeThe confusion arises due to the fact that SBA Composer makes a particular choice on the meaning of the point (0,0,0), while a dataset that is said to be aligned to the atlas may have a different idea of what the point (0,0,0) represents. The origin of the real-world space is defined as the point (0,0,0) in this enclosing box. SBA Composer defines for each supported atlas an enclosing box that consists of three pairs of values that contain the minimum and maximum coordinate along each anatomical axis. This is one of the most confusing aspects of image alignment. When either the user or the BAS meta data overrides the detected orientation, scaling and/or origin landmark, then A is recomputed by constructing T, R* and S from the new values, while keeping Z as is. Z is the 'remainder' matrix that contains all components of A that cannot be represented by translation, re-orientation and scaling.It uses only axis flips and multiples-of-90-degree rotations. R* is the rotation matrix that reorients the data from its original orientation to RAS.We then define a matrix R* that re-orients data from these orientation axes to RAS, and use it to find the 'remainder matrix' Z: Then we can apply the inverse rotation to find the orientation axes that align best with the brain in its original space. If we assume that R indeed rotates the data to RAS orientation (or for non-Nifti1 files, the specified orientation),
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