Your error states that the problem is line 926, but I think the problematic line should be 927 if your are running the program you took a screenshot of. So perhaps you are not running the new fixed function. Check your Matlab path.
Either way you should add a line with just "keyboard" before line 927 or 926 ..
and then just run a "whos" to check all the dimensions of the index vector "Ndx" and the variables used to make "Ndx" in lines "921-923", especially 922, and check that the "Kernel" matrix size also makes sense. I guess "NumDipoleComponents(kk)" should be 1 for every chunk of source space with fixed orientation dipoles (i.e., a surface with dipoles fixed to normals) and should be 3 (or 2 if using spherical head model) for volumetric source space chunks. Also check that the corresponding "NumDipoles(kk)"'s make sense. Hope you get it working. Best, Rey