<div dir="ltr">ColorMap0 is equal to EVec0 x FA<div style>This is what people use. The assignment of the color; x = red, y=green, z=blue is arbitrary, but this scheme is most widely used.</div><div style><br></div><div style>
ColorMap1 is EVec1xFA</div><div style>ColorMap2 is Evec2xFA</div><div style><br></div><div style>These are rarely used.</div><div style><br></div><div style>ColorMap0 is used for visual evaluation and rarely used for quantification purpose.</div>
<div style>As a matter of fact any EVec are rarely used for quantification purposes except for tractography.</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Apr 10, 2013 at 11:31 PM, skhekmat <span dir="ltr"><<a href="mailto:skhekmat@hotmail.com" target="_blank">skhekmat@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">One quick question, which color coded orientation map is important for display? It creates three color map files after tensor calculation, ( Looks same as when I create by multiplying eigen vector with FA map). I have seen people displaying different color coded maps . What is proper representation of directional coded FA map?<u></u><u></u></span></p>
<p class="MsoNormal"><a name="13df72728571c072__MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></a></p><div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a> [mailto:<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>] <b>On Behalf Of </b>susumu mori<br>
<b>Sent:</b> Wednesday, April 10, 2013 3:05 PM<br><b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br><b>Subject:</b> Re: [Mristudio-users] saving gradient file<u></u><u></u></span></p></div><p class="MsoNormal">
<u></u> <u></u></p><div><p class="MsoNormal">I simply save it as a text file and cut&paste.<u></u><u></u></p><div><p class="MsoNormal">You can also try *.dpf format.<u></u><u></u></p></div></div><div><p class="MsoNormal" style="margin-bottom:12.0pt">
<u></u> <u></u></p><div><p class="MsoNormal">On Wed, Apr 10, 2013 at 1:22 PM, skhekmat <<a href="mailto:skhekmat@hotmail.com" target="_blank">skhekmat@hotmail.com</a>> wrote:<u></u><u></u></p><div><div><p class="MsoNormal">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hello DTI Studio users</span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Is there any way to save my own gradient file(s) on the computer?</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks</span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Ned </span><u></u><u></u></p>
<p class="MsoNormal"><a name="13df72728571c072_13df4fbc83be2c26__MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></a><u></u><u></u></p><div><div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a> [mailto:<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>] <b>On Behalf Of </b>skhekmat<br>
<b>Sent:</b> Friday, April 05, 2013 2:02 PM<br><b>To:</b> 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'<br><b>Subject:</b> Re: [Mristudio-users] masking</span><u></u><u></u></p></div></div><p class="MsoNormal">
<u></u><u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hello Susumu</span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks for providing suggestions, I tried to follow that, I do have some questions on that…</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p><div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a> [<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mailto:mristudio-users-bounces@mristudio.org</a>] <b>On Behalf Of </b>susumu mori<br>
<b>Sent:</b> Thursday, April 04, 2013 5:34 PM<br><b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br><b>Subject:</b> Re: [Mristudio-users] masking</span><u></u><u></u></p></div><p class="MsoNormal"> <u></u><u></u></p>
<div><p class="MsoNormal">Hi Ned,<u></u><u></u></p><div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal">The simplest masking you can use is the intensity threshold.<u></u><u></u></p></div><div><p class="MsoNormal">
When you click "tensor" calculation, there is a section to define an intensity threshold. This should suppress most of the background noise floor.<u></u><u></u></p></div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">My question is, In DTI map option ( in tensor calculation) does it create and save a mask file using threshold option 10 %) somewhere explicitly in my computer? If so, I could not find it.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal">More sophisticated method is to apply for skull-strip.<u></u><u></u></p>
</div><div><p class="MsoNormal">You can do this at the tensor calculation by loading a masking file, again, within the tensor calculation window.<u></u><u></u></p></div><div><p class="MsoNormal">The brain mask file should contain 1/0 information. <u></u><u></u></p>
</div><div><p class="MsoNormal"><span style="color:#1f497d"> </span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Using this option, I created a roi mask file in binary format and but unable to load at tensor calculation, may be it reads only rec file</span><u></u><u></u></p>
</div><div><p class="MsoNormal">Or, you can skull-strip after tensor calculation.<u></u><u></u></p></div><div><p class="MsoNormal"><span style="color:#1f497d"> </span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Using this, is a better option, after tensor calculation, I do not know how to apply to resultant images. </span><u></u><u></u></p>
</div><div><p class="MsoNormal">For the skull-strip, you can use any software out there. We use our own skull-strip function in RoiEditor.<u></u><u></u></p></div><div><p class="MsoNormal">You can load FA, trace, and other images with b0 or iDWI (the sum of all DWIs you can calculate in DtiStudi).<u></u><u></u></p>
</div><div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal">You can use b0 or iDWI for skull stripping and the resultant masking is applied to all loaded images.<u></u><u></u></p></div><div><p class="MsoNormal">
<u></u><u></u></p></div><div><p class="MsoNormal">Hope this will help.<u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal">Susumu<u></u><u></u></p></div></div><div><p class="MsoNormal" style="margin-bottom:12.0pt">
<u></u><u></u></p><div><p class="MsoNormal">On Thu, Apr 4, 2013 at 12:34 PM, skhekmat <<a href="mailto:skhekmat@hotmail.com" target="_blank">skhekmat@hotmail.com</a>> wrote:<u></u><u></u></p><div><div><p class="MsoNormal">
<span style="color:#1f497d">Hello All</span><u></u><u></u></p><p class="MsoNormal"><span style="color:#1f497d">Is there any function to create a mask in DTI studio, so that I will apply in Tensor mapping? I could create using other softwares, however, transformation causes so many issues.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="color:#1f497d">Thanks</span><u></u><u></u></p><p class="MsoNormal"><span style="color:#1f497d">Ned</span><u></u><u></u></p></div></div><p class="MsoNormal" style="margin-bottom:12.0pt"><br>
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