First, thank you for your work in creating a toolbox that will allow creation of a custom TPM file. It is a very interesting toolbox, but I feel I may be missing something in the instructions.
To be specific, I am having issues in understanding exactly what images to use as the input when creating the TOM.mat file.
I think I am suppose to use the normalized, unmodulated segmented files for each tissue type (c1* c2*, etc). Is this correct?
If one uses the VBM8 toolbox, there is no option to write out all 6 classes of images, only gm, wm and csf.
How does one get the other tissue files?
If you use the results of new segment, as per the current VBM instructions in SPM8, one gets nonlinear transformed segmented images that may have some segmentation artifacts (at least that is the case for many of my elderly subjects).
So if I want to create a 6 tissue TPM.nii file, what images should I use?