<div dir="ltr"><div style="font-size:12.8000001907349px">Dear all,</div><div style="font-size:12.8000001907349px">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.</div><div style="font-size:12.8000001907349px">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, <a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2014-May/000993.html" target="_blank">http://www.nitrc.org/pipermail/mrtrix-discussion/2014-May/000993.html</a>, 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.</div><div style="font-size:12.8000001907349px">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, <a href="http://www.brain.org.au/software/mrtrix/tractography/tracking.html" target="_blank">http://www.brain.org.au/software/mrtrix/tractography/tracking.html</a>, which is mainly to obtain FA. As such, some of the options may not make sense.</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">tensor_metric dt.mif -num 1,2,3 -value MD_val.mif</div><div style="font-size:12.8000001907349px">erode mask.mif -npass 3 - | mrmult MD_val.mif - - | threshold - -abs 0.4 sf_MD_val.mif </div><div style="font-size:12.8000001907349px">estimate_response dwi.mif sf_MD_val.mif -grad b.txt response_md.txt</div><div style="font-size:12.8000001907349px">csdeconv dwi.mif response_md.txt -lmax 8 -grad b.txt -mask mask.mif CSD8_MD.mif<span style="white-space:pre-wrap"> </span></div><div style="font-size:12.8000001907349px">streamtrack SD_PROB CSD8_MD.mif -seed leftM1.mif -include ccmask.mif -include rightM1.mif -mask mask.mif lm1_rm1_PROB_MD.tck</div><div style="font-size:12.8000001907349px">tracks2prob -template MD_val.mif lm1_rm1_PROB_MD.tck FA_masklm1_rm1_PROB_MD.mif</div><div style="font-size:12.8000001907349px">threshold FA_masklm1_rm1_PROB_MD.mif FA_masklm1_rm1_PROB_MDthr.mif</div><div style="font-size:12.8000001907349px">mrstats MD_val.mif -mask FA_masklm1_rm1_PROB_MDthr.mif -dump FA_masklm1_rm1_PROB_MDthr.txt</div><div style="font-size:12.8000001907349px">(Q2) Are these steps appropriate?</div><div style="font-size:12.8000001907349px">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? </div><div style="font-size:12.8000001907349px">Thank you for your help in advance.</div><div style="font-size:12.8000001907349px">Matt</div></div>