Hi, Neuro-

It's a bit hard for me to see what it would mean to calculate distances between locations in different spaces... I guess you have some ROI/location defined in one space, and another defined from another study in another space?

A few things to note; we have standard meshes for different standard spaces available, including MNI and Talairach-Tournoux:
[afni.nimh.nih.gov]
[afni.nimh.nih.gov]
[afni.nimh.nih.gov]

Once you find the node index associated with a coordinate location in one space, you can use that node index on any AFNI/SUMA-standardized mesh and it should refer to the same anatomical location in that brain-- that is what it means to be on a "standardized" mesh. This hsould provide you what you need:
+ find the index for some locations in whatever coordinate space you want, and then
+ calculate the distance between your desired index pairs on any of these standardized meshes, in your desired coordinate space.

Just make sure that you know what system your coordinates are defined in-- again, the default is DICOM (=RAI), but you can also flag to use other coord systems.

--pt