[Mrtrix-discussion] fiber statistics-MD, AD, RD

[HF]

Dear all,
I have a couple of questions regarding CSD tractgraphy and fiber
statistics. As I am new to this field, what I say is not clear and/or
doesn't make sense. If this is the case, my apolgy. Below you will see my
quesitons (Q) in the context.
I am trying to obtain MD, AD, and RD for the tracts we contrcuted using
CSD. I am aware that this question was raised before,
http://www.nitrc.org/pipermail/mrtrix-discussion/2014-May/000993.html, but
I would like to know the exact steps including command and paramters I
should be using. (Q1) I am also guessing that I need to obtain L1, L2, and
L3 and then calculate MD, AD, and RD in excel or something.  I would
apprecite if someone could help me out.
Here is the commands I think it's right at this stage. The CSD I ran was to
see the tracts between M1s. Note that I follow the steps described in here,
http://www.brain.org.au/software/mrtrix/tractography/tracking.html, which
is mainly to obtain FA. As such, some of the options may not make sense.

tensor_metric dt.mif -num 1,2,3 -value MD_val.mif
erode mask.mif -npass 3 - | mrmult MD_val.mif - - | threshold - -abs 0.4
sf_MD_val.mif
estimate_response dwi.mif sf_MD_val.mif -grad b.txt response_md.txt
csdeconv dwi.mif response_md.txt -lmax 8 -grad b.txt -mask mask.mif
CSD8_MD.mif
streamtrack SD_PROB CSD8_MD.mif -seed leftM1.mif -include ccmask.mif
-include rightM1.mif -mask mask.mif lm1_rm1_PROB_MD.tck
tracks2prob -template MD_val.mif lm1_rm1_PROB_MD.tck
FA_masklm1_rm1_PROB_MD.mif
threshold FA_masklm1_rm1_PROB_MD.mif FA_masklm1_rm1_PROB_MDthr.mif
mrstats MD_val.mif -mask FA_masklm1_rm1_PROB_MDthr.mif -dump
FA_masklm1_rm1_PROB_MDthr.txt
(Q2) Are these steps appropriate?
If I ran these commands, the command promt displays mean, sd, min, max,
count (Q3, what this count? fiber counts?). in three lines for ch0-2.  But
the text file contains only one columns. (Q4) What are these numbers in the
text file?
Thank you for your help in advance.
Matt
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