Hello,

I want to quantify the accuracy of alignment for surfaces that are aligned to std.141 during the normal SUMA pipeline. In other words, how much error is there in the alignment, akin to a cost metric that is produced in traditional anatomical alignment.

I think way to evaluate alignment is to use the `std.141.*.MI.1D` files that are produced by @SUMA_Make_Spec_FS. I think that this file measures the mutual information cost of the alignment of each node to the std.141 mesh; however, I am not sure this is true. It seems to be created by MapIcosahedron (https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/MapIcosahedron_sphx.html). On that web page it mentions these files in the following:
"Write a file showing the mapping of each
node in the icosahedron to the closest
three nodes in the original mesh.
The file is named by the prefix of the output
spec file and suffixed by MI.1D"

I am aware that this is only one type of metric for alignment and other procedures, like using the Enigma QC, could be an alternative.

Could you please provide clarification about what these MI.1D files represent and whether they would be appropriate for evaluating alignment?

Thanks,
Cameron