Hi, Mark,
I'm having a similar issue as reported by Teresa. In my case, my functional EPIs have restricted field of view (oblique slab, aligned with AC-PC, 8.8cm thick). I've been running my analyses without field map correction, and using the 2-step registration process, where my Initial structural image is a whole-brain EPI image (as recommended in the FSL tutorial).
I am now trying to incorporate fieldmap correction, but I'm unsure on how to do this together with the 2-step registration. If I proceed the same way as before but with the added option of B0 unwarping in the pre-processing tab, unwarping ends up not working well (it reports not being able to open the matrix files, e.g. ../example_func2highres.mat). However, if I uncheck the Initial registration option, unwarping works fine, but registration is suboptimal.
I was wondering if there is any way for me to perform the 2-step registration (initial+main structural images), while at the same time performing B0 unwarping. Do I need to manually unwarp the Initial whole-brain EPI image?
Thank you very much,
--Marcelo Mattar
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