Dear Users,
We're working with some old functional data collected with a limited field of
view that prioritised inferior regions.
We have a partial FoV anatomical with the same number of slices as the
functional and a full brain anatomical.
While I can successfully register the partial anatomical to the full brain
anatomical, I'm having no luck with the partial functional to partial
anatomical.
I have tried all manner of combinations of with/without skull, 3/6 DOF,
nosearch/full search, the various fsl schedules including ztrans only, various
cost options, identity transform etc, but no matter what I try, I get the same
result - the functional is placed too low relative to the anatomical.
I have attached a screen shot, where I have tried to indicate the superior
border of the cerebellum, and the space between the cerebelllum, splenium
and occipital lobe (green for the anatomical, blue for the registered
functional).
Any thoughts or advice would be very much appreciated.
For example, is it possible to manually place the functional into alignment
with the partial anatomical, then write the translations into a flirt matrix
that can be concatenated with the partial-to-full-brain anatomical matrix? I
can do the manual shifting using AFNI's 3drefit, which allows you to shift the
brain around in x, y and z using mm space, but I can't see how those mm
values translate into FLIRT matrix values.
These data were previously analysed using SPM, which I'd like to avoid ;)
Thanks a million!
Clare
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