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Dear Steve,
I'm currently working with FSL-VBM as well, rewriting the scripts so they work with GNU parallel. I also wanted to try out the approach for white matter. However, apart from changing the segmentation output, the second registration step also refers to a FNIRT configuration file called "GM_2_MNI152GM_2mm.cnf". Is there a WM version of this file? Or how would I proceed to create one myself?
Regards,
Ralph