Doesn't that only move the center of the image (e.g. move the center from center of mass to center of the volume) but not moving the data itself?

Doing a simple 3dresample command is problematic since that can cut of parts of the brain. What seems to work is this:

for i in * ; do 3dAllineate -cmass -warp shift_only -base ../new_template.nii.gz -source $i -prefix rs_$i ; done

The -warp shif_only option in combination with the -cm option seems to move the brain into the center of the new volume and it has the right resolution. No rotation or further alignment seem to have taken place. This basically does what I want - I just want to know if there is a better option or a flag I should use.

Adding image of original image, template and resulting image



Edited 2 time(s). Last edit at 09/23/2020 09:11AM by Robin.