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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='color:#1F497D'>Dear Vikash,<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Thanks for your quick reply. I think I am getting the correct FA values inside the brain, but I will check them just in case. I have already mask the image, so the image I visualize is the correct one, but I was just asking in the mailing list just in case there was a specific reason. <o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Regards,<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Alba<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 width="60%" style='width:60.0%;border-collapse:collapse'><tr><td width=260 valign=top style='width:195.0pt;padding:3.75pt 0cm 0cm 3.75pt'><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 width="100%" style='width:100.0%'><tr><td style='padding:0cm 0cm 0cm 0cm'><p class=MsoNormal><b><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#1F497D'>Alba Garin Muga</span></b><span style='font-size:12.0pt;color:#1F497D'><o:p></o:p></span></p></td></tr><tr><td style='padding:0cm 0cm 0cm 0cm'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#1F497D'>Computer Science PhD Student</span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:#1F497D'><o:p></o:p></span></p></td></tr><tr><td style='padding:0cm 0cm 0cm 0cm'><p class=MsoNormal><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#1F497D'>Applied Mechanics Department</span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:#1F497D'><o:p></o:p></span></p></td></tr><tr><td style='padding:0cm 0cm 0cm 0cm'><p class=MsoNormal style='margin-top:6.0pt;mso-margin-bottom-alt:auto'><span lang=ES style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#1F497D'>Paseo Manuel Lardizabal, 15<br>20018 Donostia-San Sebastian. </span><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#1F497D'>Spain<br>Tel. +34 943 212 800 (Ext. 2111)<br>Fax: +34 943 213 076<br>Web: </span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:#1F497D'><a href="http://www.ceit.es/"><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif"'>www.ceit.es</span></a></span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:#1F497D'><o:p></o:p></span></p></td></tr></table></td><td width=659 valign=top style='width:494.25pt;padding:0cm 0cm 0cm 0cm'><p class=MsoNormal><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#1F497D'><img border=0 width=227 height=120 id="_x0000_i1029" src="cid:image001.gif@01CE15AA.EEBC3B20" alt="http://intranet.ceit.es/PlantillasCEIT/ImagenCorporativa/Firmas/firma_ceit.gif"></span><span style='font-size:12.0pt;color:#1F497D'><o:p></o:p></span></p></td></tr><tr><td colspan=2 valign=top style='padding:3.75pt 0cm 0cm 3.75pt'><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 width="100%" style='width:100.0%'><tr><td width="4%" valign=top style='width:4.0%;padding:0cm 0cm 0cm 0cm'><p class=MsoNormal><span style='color:#1F497D'><img border=0 width=31 height=30 id="_x0000_i1028" src="cid:image002.jpg@01CE15AA.EEBC3B20" alt=Verde></span><span style='font-size:12.0pt;color:#1F497D'><o:p></o:p></span></p></td><td width="96%" style='width:96.0%;padding:0cm 0cm 0cm 0cm'><p class=MsoNormal><span lang=ES style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#009900'>Antes de imprimir este e-mail piense bien si es necesario hacerlo. </span><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#009900'>El medioambiente es cosa de todos.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#009900'>Before printing this e-mail ask yourself if you really need a hard copy. We are all responsible for the environment.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#009900'>E-mail hau inprimatu baino lehen</span><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#009900'> egiaztatu inprimatzeko beharra. </span><span lang=ES style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#009900'>Ingurumena guztion ardura da</span><span style='font-size:12.0pt;color:#1F497D'><o:p></o:p></span></p></td></tr></table></td></tr></table><p class=MsoNormal><span lang=ES style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><div><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"'> Vikash Gupta [mailto:vikash.gupta@inria.fr] <br><b>Sent:</b> jueves, 28 de febrero de 2013 10:41<br><b>To:</b> Garin, Alba<br><b>Cc:</b> insight-users@itk.org<br><b>Subject:</b> Re: [Insight-users] itk::DiffusionTensor3D fa map<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><span style='color:black'>Hi<br>No it is highly unlikely that the FA in the air will be 0.6. o.6 is a high FA and should mostly correspond to WM. I will suggest to mask the image, because the background is generally noise and the tensors from Noise (air) does not hold nay meaning. <o:p></o:p></span></p><div><p class=MsoNormal><span style='color:black'>Also, may be check manually for a voxel or two inside the brain if you are getting correct FA. <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>Vikash<o:p></o:p></span></p><div class=MsoNormal align=center style='text-align:center'><span style='color:black'><hr size=2 width="100%" align=center id=zwchr></span></div><blockquote style='border:none;border-left:solid #1010FF 1.5pt;padding:0cm 0cm 0cm 4.0pt;margin-left:3.75pt;margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal style='margin-bottom:12.0pt'><b><span style='font-family:"Helvetica","sans-serif";color:black'>From: </span></b><span style='font-family:"Helvetica","sans-serif";color:black'>"Alba Garin" <<a href="mailto:agarin@ceit.es">agarin@ceit.es</a>><br><b>To: </b><a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br><b>Sent: </b>Thursday, February 28, 2013 10:15:43 AM<br><b>Subject: </b>[Insight-users] itk::DiffusionTensor3D fa map</span><span style='font-size:12.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>Dear all,<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>I am computing different DTI maps from an Image with itk::DiffusionTensor3D pixel type. If I get MD, Trace, First Eigenvalue and other maps, I get a correct map, but If I compute the FA map, I get high values (0.6) in the air part of the image (around the brain). I mean, even the brain can be distinguished from the air, there are values in the air. Is this normal? Have this happened to anyone before?<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>Thanks in advance.<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>Regards,<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>Alba<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 width="60%" style='width:60.0%;border-collapse:collapse'><tr><td width=260 valign=top style='width:195.0pt;padding:3.75pt 0cm 0cm 3.75pt'><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 width="100%" style='width:100.0%'><tr><td style='padding:0cm 0cm 0cm 0cm'><p class=MsoNormal><b><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif"'>Alba Garin Muga</span></b><o:p></o:p></p></td></tr><tr><td style='padding:0cm 0cm 0cm 0cm'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif"'>Computer Science PhD Student</span><o:p></o:p></p></td></tr><tr><td style='padding:0cm 0cm 0cm 0cm'><p class=MsoNormal><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif"'>Applied Mechanics Department</span><o:p></o:p></p></td></tr><tr><td style='padding:0cm 0cm 0cm 0cm'><p class=MsoNormal style='margin-top:6.0pt;mso-margin-bottom-alt:auto'><span lang=ES style='font-size:8.0pt;font-family:"Tahoma","sans-serif"'>Paseo Manuel Lardizabal, 15<br>20018 Donostia-San Sebastian. </span><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif"'>Spain<br>Tel. +34 943 212 800 (Ext. 2111)<br>Fax: +34 943 213 076<br>Web: </span><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><a href="http://www.ceit.es/" target="_blank"><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif"'>www.ceit.es</span></a></span><o:p></o:p></p></td></tr></table></td><td width=659 valign=top style='width:494.25pt;padding:0cm 0cm 0cm 0cm'><p class=MsoNormal><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif"'><img border=0 width=227 height=120 id="Picture_x0020_1" src="cid:image001.gif@01CE15AA.EEBC3B20" alt="http://intranet.ceit.es/PlantillasCEIT/ImagenCorporativa/Firmas/firma_ceit.gif"></span><o:p></o:p></p></td></tr><tr><td colspan=2 valign=top style='padding:3.75pt 0cm 0cm 3.75pt'><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 width="100%" style='width:100.0%'><tr><td width="4%" valign=top style='width:4.0%;padding:0cm 0cm 0cm 0cm'><p class=MsoNormal><img border=0 width=31 height=30 id="Picture_x0020_2" src="cid:image002.jpg@01CE15AA.EEBC3B20" alt=Verde><o:p></o:p></p></td><td width="96%" style='width:96.0%;padding:0cm 0cm 0cm 0cm'><p class=MsoNormal><span lang=ES style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#009900'>Antes de imprimir este e-mail piense bien si es necesario hacerlo. </span><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#009900'>El medioambiente es cosa de todos.</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#009900'>Before printing this e-mail ask yourself if you really need a hard copy. We are all responsible for the environment.</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#009900'>E-mail hau inprimatu baino lehen egiaztatu inprimatzeko beharra. </span><span lang=ES style='font-size:8.0pt;font-family:"Tahoma","sans-serif";color:#009900'>Ingurumena guztion ardura da</span><o:p></o:p></p></td></tr></table></td></tr></table><p class=MsoNormal><span lang=ES style='color:black'> </span><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Helvetica","sans-serif";color:black'><br>_____________________________________<br>Powered by <a href="http://www.kitware.com">www.kitware.com</a><br><br>Visit other Kitware open-source projects at<br><a href="http://www.kitware.com/opensource/opensource.html">http://www.kitware.com/opensource/opensource.html</a><br><br>Kitware offers ITK Training Courses, for more information visit:<br><a href="http://www.kitware.com/products/protraining.php">http://www.kitware.com/products/protraining.php</a><br><br>Please keep messages on-topic and check the ITK FAQ at:<br><a href="http://www.itk.org/Wiki/ITK_FAQ">http://www.itk.org/Wiki/ITK_FAQ</a><br><br>Follow this link to subscribe/unsubscribe:<br><a href="http://www.itk.org/mailman/listinfo/insight-users">http://www.itk.org/mailman/listinfo/insight-users</a><o:p></o:p></span></p></blockquote><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></p></div></div></div></body></html>