Package that provides tools for brain Lithium MRI pre-processing.

Transform a SPM normalization field to a FSL field.

For the deformation fields generated in SPM, the values in each of the three components (ie (:,:,:,1,1), (:,:,:,1,2) and (:,:,:,1,3) ) encode the x,y,z coordinates of the corresponding location (in units of mm).

SPM conventions: 1) The file encodes the mapping rather than displacement fields for a couple of reasons: a) Even in 2012, many people still seem to think that displacements can be combined by addition or subtraction, rather than by composing or inverting the mappings. (Attempting to compose deformations by adding the displacement fields would be analogous to saying 2*2=3 or 3*3=5). Using the mapping instead of the displacements would (I hope) make this abuse a bit less likely. b) It saves needing to encode an additional affine transform matrix for dealing with the identity transform to which the displacements are added. This makes life simpler. 2) It encodes coordinates in mm, rather than voxels. If the mapping was to voxels, it would not work so well for images that are in alignment via the matrices encoded by the sform or qform fields. Also, if the mapping is to voxels, the values would depend on whether the first voxel in the file is denoted as 1,1,1 (as in MATLAB, Fortran or SPM) or as 0,0,0 (as in C or FSL). The mm coordinates are unambiguous - providing the sform (or sform) fields of the image that the deformation points to is filled in.

The bad news here is that you do need to use the sform (qform) information to convert from SPM to FSL conventions. In FSL we can use either absolute coordinates (as is used in SPM) or relative ones. However, our mm coordinate system is not the same, so you’ll need to map between FSL’s and SPM’s if you want to get the warp correct.

The problem you are experiencing will be about coordinate system conventions. Our mm coordinate system is just a scalar multiple of the voxel coordinates if the image has a negative sform (or qform) determinant. If the determinant of the sform (or qform) matrix is positive then is it the same except that the x-voxel-coordinate is flipped first (0 to N-1 becomes N-1 to 0). Note that this means that our origin is in the 0,0,0 voxel (the centre of the voxel) and that we do not use the qform or sform information (except for the sign of the determinant). If you can figure out what the SPM conventions are then you should be able to adjust for this, although it may not be easy.

References

https://github.com/nipy/nitransforms https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;ed6a4473.1208