Dear AFNI,

Thank you for your help previously in getting animal_warper to run.

The results generally look great, however we are interested in mapping connections of small hippocampal subfields and so it is particularly important for our analyses that these small sub-regions (taken from the D99 atlas) are registered precisely to our native T1w's.

I have attached an example picture below of where the results are not ideal. Do you have any recommendations for improving the alignment between our native space T1w images and the D99 atlas/ template? Is this simply a case of our image quality not allowing for better alignment, or perhaps is it best that we just go in and manually 'correct' the places where alignment has not worked as intended?

I have attached a QC image and an example of where I think registration hasn't gone to plan. The two ROI's are CA1 and Subiculum complex (created by adding all of the subiculum ROI's together). Please let me know if it is useful to see any other images.

Many thanks in advance,
Sam