Hi, 

Im planning to use the Clinical toolbox in order to mask out stroke lesions. I have used itk Snap to mask out lesions, but I am not sure how to add this mask into the clinical toolbox so that the normalization will mask out the lesion. 

Itk snap creates a segmentation of the lesion which may be saved as a nifti file. I have read the manual but still can´t really understand how to enter this into the clinical toolbox. 

Is it enough if I add the lesion/segmentation (not drawn on any T1 or T2 image) into "lesion maps" in the Batch editor? How do I know if it works? Should I somehow instruct SPM to avoid the values where the segmentation is and how would I do that? I Please see attached file. 



Thank you in advance!

/Hanna