<div dir="ltr"><div><div>Hi Helen,<br><br></div>What you're seeing is (probably) correct: FAs larger than 1 and ADCs below 0 can appear due to the tensor estimation in MRtrix being a simple (unconstrained) linear least squares one. The tensors are not explicitely constrained to be positive definite, and thus negative eigenvalues might appear. When one or more eigenvalues of a given tensor are negative, the FA can go beyond 1, while the ADC can go below 0.<br>
<br></div>Cheers,<br>Thijs<br><div><div><div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><span style="color:rgb(68,68,68)"><b><font size="4">Thijs Dhollander</font><br><font><a href="mailto:thijs.dhollander@gmail.com" target="_blank">thijs.dhollander@gmail.com</a><br>
Tel. +32 475 36 44 27</font></b><br><font size="1">Medical Image Computing (MIC), ESAT-PSI, Department of Electrical Engineering, KU Leuven</font></span></div></div>
<br><br><div class="gmail_quote">On Fri, Mar 21, 2014 at 10:10 PM, Helen Carlson <span dir="ltr"><<a href="mailto:Helen.Carlson@albertahealthservices.ca" target="_blank">Helen.Carlson@albertahealthservices.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div link="blue" vlink="purple" lang="EN-CA">
<div>
<p class="MsoNormal">Hello all,<u></u><u></u></p>
<p class="MsoNormal">I would like to determine the average FA and ADC values for a given track (in this case, the arcuate). So I followed previous directions posted here and have used the following commands on my arcuate which successfully creates a probability
mask for FA and ADC:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">tracks2prob –template fa.mif Arcuate.tck FA_mask.mif<u></u><u></u></p>
<p class="MsoNormal">tracks2prob –template adc.mif Arcuate.tck ADC_mask.mif<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I then used mrstats to get the average, max, min etc of the tracks by using these commands:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">mrstats fa.mif –mask FA_mask.mif<u></u><u></u></p>
<p class="MsoNormal">mrstats adc.mif –mask ADC_mask.mif<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Which also seemed to work except that I was expecting my FA to range from 0.1 to 1.0 (approximately). Instead, the FA values have a min of 0 and a max of 1.13. In addition, my ADC values have a negative minimum (-0.0024). It seems these
values are out of range and do not make sense but I do not know what I am doing wrong.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thanks in advance for any help<u></u><u></u></p>
<p class="MsoNormal">Helen<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><b><span style="color:#365f91">Helen Carlson, Ph.D<u></u><u></u></span></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#365f91">Neuroimaging Research Associate<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#365f91">Calgary Pediatric Stroke Program & Neuropsychology<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#365f91">Alberta Children's Hospital<u></u><u></u></span></p>
</div>
<br>
<hr>
<font color="Gray" face="Arial" size="1">This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is
strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you.<br>
</font>
</div>
<br>_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
<br></blockquote></div><br></div></div></div></div></div>