Hi,
Im running FIRST on a group of participants, and for most of them the segmentations are very good. However, for one of the participants the caudate is not properly estimated (the segmentation is smaller than the actual image). I checked the registration and the participant's caudate does not overlap well with the MNI brain. I took a look at the first_flirt options but Im not sure which option would be most appropriate to fix this issue. Could you recommend how the registration could be improved? Should I try to use regular flirt and use this transformation as transformation matrix when I run run_first_all?
Thank you,
Anastasia
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