<p dir="ltr">Hi Matt,</p>
<p dir="ltr">You can actually get all the values you need within MRtrix - no need for Excel:</p>
<p dir="ltr">$ tensor_metric dt.mif -adc MD.mif -fa FA.mif -num 1,2,3 -value D[1:3].mif<br>
$ mradd D2.mif D3.mif - | mrconvert - -scale 0.5 RD.mif</p>
<p dir="ltr">At this point, you'd have the MD & FA maps, and each eigenvalue as a separate map (D1.mif -> D3.mif). D1.mif is the AD, and the second command gets you RD explicitly as (D2+D3)/2.</p>
<p dir="ltr">After that, it looks like you're using the first eigenvalue to determine the mask for the response function estimation. I'm not sure whether you have a particular reason to do that, but the general recommendation (at least in this version of MRtrix) is to use the FA map, thresholded at around 0.7 (ideally you want to end up with ~200-300 voxels in the mask, placed in regions you'd expect to contain predominantly single fibre populations). I notice you say you followed the instructions in the documentation to get the FA, but nowhere is the FA computed in your commands...</p>
<p dir="ltr">Most other commands look fine until your threshold command - really you want to set an explicit threshold value here using the -abs option, otherwise you'll get a variable threshold depending on exactly how the automatic threshold determination decided to work on that particular image, which wouldn't be great for cross-subject analysis. What threshold to use is a bit of an arbitrary decision, but the main idea is to remove spurious voxels, so try different values until you're satisfied that it's doing a decent job.</p>
<p dir="ltr">Overall, the general approach seems fine otherwise. The output of mrstats's count value is the number of voxels in the mask you supplied. The numbers in the file produced with the -dump option are just the voxel intensities in the image within the mask. You supplied a 4D, 3 volume image, but you get all the values for all 3 volumes as one big vector. You'd be better off using mrstats for each of the FA, MD, AD & RD maps independently if you need to use the -dump option...</p>
<p dir="ltr">Cheers,<br>
Donald</p>
<div class="gmail_quot<blockquote class=" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><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>
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