Hello
I have a similar problem, where a dataset of 223 subjects was processed in MNI space, but I can not do any voxel-based connectivity measure.
Can you help me with this?

ERROR DESCRIPTION:
Error using spm_check_orientations (line 65)
The orientations etc must be identical for this procedure.
Error in spm_spm (line 323)
spm_check_orientations(VY);
Error in conn_process (line 5008)
SPM=spm_spm(SPM);
Error in conn_process (line 60)
case 'results_voxel', [varargout{1:nargout}]=conn_process(16,varargin{:});
Error in conn (line 11573)
conn_process('results_voxel','readsingle','voxel-to-voxel');
Error in conn (line 10650)
elseif state==3, conn gui_results_wholebrain_vv;
CONN20.b