Hi Matthew

In the latest release there is also a (still in development) possible way to create new TPM files informed by a lesion mask. For that you may simply use the syntax:

   conn_createtpm( lesionfile, anatfile)

where 'lesionfile' is your lesion mask, and 'anatfile' is an anatomical image of the same subject and in the same space as your lesion mask. This will create a new TPM.nii file (named by default lesionTPM.nii and located in your current directory) that includes a 7th tissue class (in addition to the standard gray/white/csf/bone/soft/air categories) characterizing the lesion. You can then use this new lesionTPM.nii file during segmentation (and normalization) to make sure that the lesion is properly taken into account during the combined normalization/segmentation procedure. See "help conn_createspm" for additional details, and this is still a work in progress so if you have a chance to try this out please let me know how it goes and/or if you run into any issues

Best
Alfonso

Originally posted by Matthew Heard: