<p dir="ltr">Hi Simon,</p>
<p dir="ltr">You can also sample values at the vertices of each track using the sample_tracks command. This produces a big text file with rows of values, one row per track.</p>
<p dir="ltr">This is actually best used in conjunction with the resample_tracks command, which is designed to regrid the tracks such that the vertices fall at equivalent levels along it. It's not the best documented command around, so might take some getting used to, but essentially you can specify a straight line by its two end points, and the number of sample points to take along it. Each track will be resampled so its vertices fall on the plane perpendicular to the line at the specified sample levels. You can also specify a 'way point' (I think it's called a midpoint in the doc) to have the resampling done along the corresponding arc of a circle through the three points, which is useful for curved tracks. Finally, there is a nifty feature that allows you to specify the endpoints and midpoint on a template, along with the warp to the subject's native space, which then allows you to resample at equivalent points in template space without leaving native space. I won't explain it here, but we used it in a paper that just got accepted in Neuroimage, I expect it'll be available online fairly soon (Samuel Groeschel is first author).</p>
<p dir="ltr">Cheers,<br>
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_quot<blockquote class=" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Simon,<div>You can use tracks2prob (with the FA map as the template) followed by a threshold to create mask of your bundle of interest. You can then use mrstats with the --mask option to compute the mean FA within this mask. </div>
<div>Cheers,<br></div><div>Dave</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 29 October 2013 12:47, Simon Baker <span dir="ltr"><<a href="mailto:simontebaker@gmail.com" target="_blank">simontebaker@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi all,<div><br></div><div>Is there a command that allows us to easily obtain tensor-based measures (e.g., mean FA) for specific fibre tract (streamline) bundles? Failing that, is there a way to save a mask image of the streamlines so that we can use this image to mask the FA map and calculate mean FA? What's the best way to obtain these measures?</div>
<div><br></div><div>Thank you,</div><div><br></div><div>Simon</div><span><font color="#888888"><div><div><br></div>-- <br><br>Simon Baker<br>PhD Candidate<br>Faculty of Medicine, Nursing and Health Sciences<br>
Monash University
</div></font></span></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div><b><font color="#ff6600">David Raffelt (PhD)</font></b></div><div><font color="#ff6600">Post Doctoral Fellow</font></div><div><br></div>
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