Dear CAT12 experts,

I would like to perform brain tissue segmentation on a dataset of stroke patients with CAT12. I learnt from the manual that I should provide as input the T1 image where the lesion is set to zero. However, I read in some forums that the lesion mask should be provided as input to the command line. Here the command I'm currently using, with T1 image=0 in correspondance of the lesion:

/Softwares/spm12/toolbox/cat12/cat_batch_cat.sh -l ${subj_folder}/STRUCT_PREP/SEGMENTATION -ns -a "cat.extopts.expertgui=1; cat.extopts.SLC=1; cat.output.GM.native=1; cat.output.WM.native=1; cat.output.CSF.native=1; cat.output.SL.native=1;" ${T1_brain_rmvdlesion} 

Is this correct or should I provide the lesion mask and the original T1 instead?

Thank you for your assistance,

Giorgia