Dear CAT Experts,
Is there a way to create a binary gray matter, white matter, and cerebrospinal fluid masks in CAT12 such that the masks are in DARTEL MNI space? I am interested in a mask that is independent of my dataset (i.e., I don't want to apply a simple threshold to my mwp* images to make a mask). I have looked into the various templates in the CAT folder and the CAT.nii atlas can be useful for making masks for cerebral cortex, cerebellum, etc. However, I did not see any explicit labeling of GM/WM/within brain CSF. Merging various ROIs across atlases is also not an appealing option...
Perhaps an apt analogy will be the "grey", "white", and "csf" files in the OldSeg toolbox or the "TPM" file in the tpm folder of SPM. Are there equivalent version in the DARTEL MNI space? Binarizing the "Template_6_IXI555_MNI152" file is perhaps one way forward, but it does not have CSF and it doesn't seem to have probabilities of tissue classes (rather intensities)...therefore what would be an ideal threshold for each image class?
Any help in this regard is appreciated!
Thanks and Regards
PB
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