Dear All, particularly John Ashburner and Mark Daglish,
We are finally dragging ourselves into the 21st century and moving all analyses to SPM2. A problem which emerges (and to which we couldn't find the answer in the archives) is how to deal with all our SPM99-specific PET ligand templates.
Our "raw" images are Analyze, L on R, +x voxel size, and get displayed in SPM2 as L on L, -x.
Creating a template from scratch in SPM2 leads to images which are Analyze, L on L, -x.
SPM2 templates (*.mnc) get displayed in SPM2 as L on L, +x - so far, so consistent.
SPM99 templates get displayed in SPM2 as L on R, -x; this situation would lead to the wrong sides being matched during normalisation. This is due to the x flipping during their construction in SPM99.
We therefore want to convert our SPM99 templates to something compatible with SPM2.
1. Are we correct in thinking that flipping the SPM99 templates in x will be sufficient? This leads to them being displayed as L on L, -x.
2. Ideally, we would like to have the (flipped, spm-2-ified '99 templates) in *mnc format and displayed as L on L, +x, like the supplied MNI/ICBM SPM2 *.mnc templates, but haven't had much luck with such conversions; for example Andrew Janke's ana2mnc from www.cmr.uq.edu.au/~rotor/software/ did not find the spm origin and we ended up with a template without origin and L on L, -x. Mark, I think you were working with Andrew some time ago on an improved version that would recognise the origin - any progress on that? Or are there any other tried & tested solutions?
3. A related question - some of our tools for SPM99 were written with 1x1x1 mm voxels, thereby ending up with a 182x218x182 matrix. They were fully compatible with the 2x2x2 mm, 91x109x91 matrix MNI/ICBM templates, and could, for example, just be resliced to 2x2x2 if need be without problems.
Due to concern about unequivocality of the origin, SPM2 writes 1x1x1mm images into a 181x217x181 matrix. Clearly only one slice has been lost in every dimension, leading to loss of symmetry - but which slice has been lost (inf or sup, right or left, ant or post)? Am I correct in thinking that, in order to avoid misplacement by one mm in each dimension, I have to renormalise the images used for the tool construction using SPM2?
Many thanks in advance as usual,
Alexander and Marie-Claude
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