Thank you Tom and Tibor, I think I understand it now.
Can I ask another question which may be related to this?
I have run these commands so far
epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres
flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat
fnirt --in=highres_head --aff=highres2standard.mat --cout=highres2standard_warp --config=T1_2_MNI152_2mm
applywarp -i highres -r standard -o highres2standard -w highres2standard_warp
convertwarp --ref=standard --premat=example_func2highres.mat --warp1=highres2standard_warp --out=example_func2standard_warp
I don't understand why --warp1 is used instead of --warp2. According to the convertwarp documentation, --warp1 seems to be the transform from structural to some group-average space, whereas --warp2 seems to be the transform to standard space. Since I want to register the functional to the standard space shouldn't I use the --warp2 parameter? Or group-average space can also mean standard space?
Thanks
Sam
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