11/28/2023 0 Comments Metaimage volume![]() ![]() The 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), Q is the orthonormal 'scale-orientation matrix': the rotation to be applied before scaling.S is a scaling matrix, with scaling/mirroring factors on its diagonal.T is a translation matrix, consisting of a unit diagonal and a translation vector in its fourth column.Obtaining the best guess starts with decomposing the matrix A into the product of four matrices: In either case, we assume for the moment that the data fits the atlas in which the user tries to import the file. Via the 'brain addressing system' (BAS) meta data. For automated imports, adjusted values can be specified Our best guess for the missing information can be adjusted. For manually imported files, the user is presented with a dialog in which ![]() In practice we often find that the orientation is not RAS, and/or that the xyzt_units field is not set. The choice of origin cannot be specified at all. In Nifti files for example, the orientation of the physical space is required to be RAS,Īnd the units are specified in the xyzt_units field. Part of this information is available in the volume file, but it is represented differently in each file format,Īnd it is often wrong or left out. Each atlas defines a set of landmarks for this purpose.
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