Hi, thanks for the kind reply
I'm trying to coregister images acquired with confocal microscopy with 25 micron isotropic resolution to the NISSL coronal Allen brain atlas (https://mouse.brain-map.org/static/atlas) obtained by converting to nifti a stack of tiff. As I said, results are almost satisfying, in particular for what regards outer edges, while there is still space for improvement in inner edges, maybe also due to the different contrast.
I will try to use the weights and penalty factors and keep you updated, thanks.
Meanwhile, is there any way you can help me with adding markers in the dataset header?
As mentioned, I tried with
3drefit -atrstring TAGSET_FLOATS "x0 y0 z0 0 0 x1 y1 z1 1 0 x2..." dataset_name
but it does not seem to work.
I would like to try to alternate stages of 3dQWarp with stages of 3dTagalign, but to do that, I have to be able to provide the tagsets to 3dTagalign

Thank you