Hello. I have a quick follow-up question to your instructions on how to
calculate FA from probabilistic tractography. In previous e-mails, I was
told to use the following commands to get this information:
avwmaths_32R pathway -thr <threshold> -bin -mul dti_FA FAmask
avwstats FAmask -M
However, I just realized that my masks for probabilistic tractography
(mode=twomasks_symm) were in anatomical space and not diffusion space;
therefore, I had to apply the diff2str.mat transform during probtrack.
Does this mean that I need to apply the diff2str.mat transform to dti_FA
before using the above commands? If so, are these the selections I would
make?
Transformation matrix = diff2str.mat
Input volume = dti_FA
Reference Volume = anat (T1 image that was used for registration), based on
existing volume
Thanks for your help. Hope you had a great holiday!
Kristen
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