Dear Jesper,
I was following your conversation with Hannah as I have sort of the same problem: I am also a bit confused about the correct input in the FEAT GUI for FNIRT...
Taking your example, FNIRT needs two structurals of the subject:
"your_structural" : Which should be non-extracted, i.e. its original form
"your_structural_brain" : Which should have been extracted, i.e. betted
As far as I understand the FEAT detail page and your previous post, I will put the "your_structural_brain" in the GUI and FNIRT will look for the "your_structural" by itself, right?
Now for the reference image (to be fed in the "standard space" field) I have chosen the "MNI152_T1_2mm_brain" (consistent with the input of subject's structural).
Unfortunately, this way the registration fails. In the "highres to standard" registration it seems that FNIRT tries to register the un-betted "your_structural" to the betted "MNI152_T1_2mm_brain". So do I have to change the input for the reference image to "MNI152_T1_2mm"?; and will that not prevent FLIRT from working?
Many thanks,
Carsten
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