<p dir="ltr">Hi Supreet,</p>
<p dir="ltr">It depends exactly what you're trying to do. There's basically two ways in MRtrix to extract DTI measures for a given tract. In both cases you'll need to create maps of the parameters you're interested in: tensor_metric is probably what you're looking for there.</p>
<p dir="ltr">One way to get the values from the track is to create a mask of the tract using tracks2prob, then thresholding the resulting image at an appropriate level. You can then use the resulting binary mask image as the -mask in mrstats, with any map you might be interested in as the main argument to that command. That basically gives you the mean value of the parameter of interest over all voxels visited by the track.</p>
<p dir="ltr">The other way is to use the combination of resample_tracks and sample_tracks. The first of these 'chops up' the tracks at equivalent locations along a given straight line (or if needed an arc of a circle), the second reads the values of a given parameter map at those locations and stores them in a text file, which you can then load up in Excel, Matlab, R, or whatever package you want. To use resample_tracks, it helps to use MRView to get suitable locations for the end points. There's also ways to use it for group analyses by specifying the end points in some template space, and providing the warp image that maps that subject to template space - see Groeschel et al, Neuroimage 2013 for details: <a href="http://www.ncbi.nlm.nih.gov/m/pubmed/24185027/">http://www.ncbi.nlm.nih.gov/m/pubmed/24185027/</a></p>
<p dir="ltr">Hope that provides enough information to get going...<br>
Cheers,</p>
<p dir="ltr">Donald</p>
<p dir="ltr">--<br>
Dr J-Donald Tournier (PhD)</p>
<p dir="ltr">Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London</p>
<p dir="ltr">A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
T: +44 (0)20 7188 7118 ext 53613<br>
W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
</p>
<div class="gmail_quote">On 23 May 2014 20:11, "Supreet kaur" <<a href="mailto:ksupreet6@gmail.com">ksupreet6@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Dear Mrtrix users,<br><br><br><div dir="ltr"><div><div>I have been running the CSD and was trying to get the fiber statistic and DTI fiber
measures such as FA, MD, eigenvalues, RD and AD values the CSD.<br><br></div><div>Is there any specific commands that need to be used in order to get these DTI measures?<br></div><div><br> I'll appreciate your response.<br>
</div>
<br></div>Thanks in advance,<br><br></div><br clear="all"><div><div><br><div>Sincerely,<br><br>Supreet kaur,</div>
<div>Biomedical research engineer,<br>Nationwide Childrens Hospital,<br>Columbus, OH<br>(614)355-6659.</div>
</div></div></div>
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