FSL Community,
I am hoping to get help and guidance on possibly constraining my TBSS analysis to just the main white matter tracts. This inquiry is based on the USC ENIGMA pipeline (http://enigma.ini.usc.edu/wp-content/uploads/DTI_Protocols/ENIGMA_TBSS_protocol_USC.pdf), which, as I understand it, allows for a more constrained analysis (via the modified ENIGMA skeleton mask) by getting rid of the smaller periphery white matter areas. Although I have read through the ENIGMA manual, how to transition back to the TBSS pipeline after things are put in ENIGMA space is still unclear, leading me to wonder if there are easier ways to do this by either: (1) putting the ENIGMA mask into my own TBSS space (i.e., MNI); or (2) creating my own mask (with my tracts of interest) using fslview and use fslmaths to apply this to my own skeleton mask. My hope by "constraining" the skeleton mask is to focus the TBSS analysis on just the major tracts that I am interested in without having the more peripheral white matter portions eating up power.
I would sincerely appreciate your input and guidance on this. Thank you in advance for your time.
Cristina
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