<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 12 (filtered medium)"><!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-CA link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hello Thijs<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thank-you for your reply to my question. I would like to quantify changes in white matter over time, specifically pre/post treatment. Is there a better way to do this than using the mean FA and ADC? Or is this measurement appropriate? <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks again<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Helen.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> mrtrix-discussion-bounces@www.nitrc.org [mailto:mrtrix-discussion-bounces@www.nitrc.org] <b>On Behalf Of </b>Thijs Dhollander<br><b>Sent:</b> March 23, 2014 9:47<br><b>To:</b> mrtrix-discussion@www.nitrc.org<br><b>Subject:</b> Re: [Mrtrix-discussion] FA and ADC values for a tract<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'>Hi Helen,<o:p></o:p></p></div><p class=MsoNormal style='margin-bottom:12.0pt'>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.<o:p></o:p></p></div><p class=MsoNormal>Cheers,<br>Thijs<o:p></o:p></p><div><div><div><div><p class=MsoNormal><br clear=all><o:p></o:p></p><div><div><p class=MsoNormal><b><span style='font-size:13.5pt;color:#444444'>Thijs Dhollander</span><span style='color:#444444'><br><a href="mailto:thijs.dhollander@gmail.com" target="_blank">thijs.dhollander@gmail.com</a><br>Tel. +32 475 36 44 27</span></b><span style='color:#444444'><br></span><span style='font-size:7.5pt;color:#444444'>Medical Image Computing (MIC), ESAT-PSI, Department of Electrical Engineering, KU Leuven</span><o:p></o:p></p></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On Fri, Mar 21, 2014 at 10:10 PM, Helen Carlson <<a href="mailto:Helen.Carlson@albertahealthservices.ca" target="_blank">Helen.Carlson@albertahealthservices.ca</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hello all,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>tracks2prob –template fa.mif Arcuate.tck FA_mask.mif<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>tracks2prob –template adc.mif Arcuate.tck ADC_mask.mif<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I then used mrstats to get the average, max, min etc of the tracks by using these commands:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>mrstats fa.mif –mask FA_mask.mif<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>mrstats adc.mif –mask ADC_mask.mif<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thanks in advance for any help<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Helen<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span style='color:#365F91'>Helen Carlson, Ph.D</span></b><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.0pt;color:#365F91'>Neuroimaging Research Associate</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.0pt;color:#365F91'>Calgary Pediatric Stroke Program & Neuropsychology</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.0pt;color:#365F91'>Alberta Children's Hospital</span><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div class=MsoNormal align=center style='text-align:center'><hr size=2 width="100%" align=center></div><p class=MsoNormal><span style='font-size:7.5pt;font-family:"Arial","sans-serif";color:gray'>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.</span><o:p></o:p></p></div><p class=MsoNormal style='margin-bottom:12.0pt'><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><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></div></div></div></div></body></html>