Dear FSL user community,
I was looking over the FLIRT user guides to make sure I understood how to correctly implement a script to register some ASL data from native space to a standard reference (after first registering to a highres structural image). To do so I know it is advisable to use the normal "control" image (or a mean of the control images if multiples), and not any calculated perfusion, CBF or CBV maps. Then I can apply the transforms for the control/mean image to the perfusion images. This would be somewhat similar to the example given in the fsl wiki pages for "using FLIRT to register a few fMRI slices", so I looked at the examples given there, especially the registration portion
convert_xfm -concat whole_func2highres.mat -omat example_func2highres.mat example_func2whole_func.mat
convert_xfm -concat highres2standard.mat -omat example_func2standard.mat example_func2highres.mat
However, from reading the convert_xfm help, it would seem these lines might have the options -concat and -omat, (and the .mat files) in the wrong order. and these two lines should probably read
convert_xfm -omat example_func2highres.mat -concat whole_func2highres.mat example_func2whole_func.mat
convert_xfm -concat example_func2standard.mat -omat highres2standard.mat example_func2highres.mat
Could some one check this for me, as I plan to do something very similar with my ASL data.
P.S. I know there is a -regfrom option for oxford_asl - but there are reasons why that did not work with this data set which are a bit too long to go into here. i will make a post about why that is, and how I fixed it shortly in the hopes it helps others (or that I get corrected if I'm doing something stupid :-))
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