Dear John,
thank you for the suggestion. Just to double check: If I understand this
correctly, DARTEL applies the second matrix (used for the alignment of the
scans during the import step) to allow for the application of the flow field
(e.g. estimated on T1 scans) to non-imported scans (e.g. DTI, fMRI) in the
native space for highdimensional normalization, under the assumption that
the original T1 scans and DTI/fMRI scans were collected in the same subject
specific native space.
Thus, if we apply the DARTEL flow fields with the "Dartel-Normalize-to-MNI"
tool (without specifying template_6.nii) to non-imported DTI scans that were
coregistered with imported GM segments (rc1 scans) rather than the "native"
c1 scans, DARTEL would wrongly apply the combination of flow fields and the
affine matrix to the DTI scans that are actually in the "inter-subject"
rigidly aligned native space rather than the individual native space?
Best regards,
Max
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