I am troubleshooting a possible misalignment in a feat directory created by another researcher using FNIRT. In this directory, example_func.nii.gz seems to not be aligned to filtered_func_data or cope1 when viewing in FSLEyes. cope1 and filtered_func_data are well-aligned to each other. Does this indicate a problem, or is this expected?
I can't see any reason for a possible misalignment except that the crop on the T1 brain extraction might be slightly overzealous, though not to a degree that I would expect a problem. But I want to extract ROIs from the cope, and don't know how to do that if it seems misaligned with example_func.
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