Hello!
Some of my participants have very large lesions due to arterial stroke and the segmentation process has incorrectly classified the lesion as grey and white matter rather than CSF. To try to adjust for this and to help with normalisation, I would like to use  Cost Function masking to individually fix the issue.  

My question is, at which point in preprocessing can I enter the lesion mask image? It does not seem to be an option in SPM12 and I prefer to use CONN. Is there a way I would be able to manually enter them somewhere?

Thanks! 

Cole