<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Hi DTI experts</div><div>Could you please explain the term skull stripping and its importance for data analysis</div><div><br>On Apr 5, 2013, at 8:03 PM, "skhekmat" <<a href="mailto:skhekmat@hotmail.com">skhekmat@hotmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><meta name="Generator" content="Microsoft Word 12 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--><div class="WordSection1"><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hello Susumu<o:p></o:p></span></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…<o:p></o:p></span></p><p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></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">mristudio-users-bounces@mristudio.org</a> [<a href="mailto:mristudio-users-bounces@mristudio.org">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<o:p></o:p></span></p></div><p class="MsoNormal"><o:p> </o:p></p><div><p class="MsoNormal">Hi Ned,<o:p></o:p></p><div><p class="MsoNormal"><o:p> </o:p></p></div><div><p class="MsoNormal">The simplest masking you can use is the intensity threshold.<o:p></o:p></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.<o:p></o:p></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.<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><p class="MsoNormal"><o:p> </o:p></p></div><div><p class="MsoNormal">More sophisticated method is to apply for skull-strip.<o:p></o:p></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.<o:p></o:p></p></div><div><p class="MsoNormal">The brain mask file should contain 1/0 information. <o:p></o:p></p></div><div><p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></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<o:p></o:p></span></p></div><div><p class="MsoNormal">Or, you can skull-strip after tensor calculation.<o:p></o:p></p></div><div><p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></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. <o:p></o:p></span></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.<o:p></o:p></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).<o:p></o:p></p></div><div><p class="MsoNormal"><o:p> </o:p></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.<o:p></o:p></p></div><div><p class="MsoNormal"><o:p> </o:p></p></div><div><p class="MsoNormal">Hope this will help.<o:p></o:p></p></div><div><p class="MsoNormal"><o:p> </o:p></p></div><div><p class="MsoNormal">Susumu<o:p></o:p></p></div></div><div><p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></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:<o:p></o:p></p><div><div><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">Hello All</span><o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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><o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">Thanks</span><o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">Ned</span><o:p></o:p></p></div></div><p class="MsoNormal" style="margin-bottom:12.0pt"><br>_______________________________________________<br>mristudio-users mailing list<br><a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a><br><a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org">mristudio-users-unsubscribe@mristudio.org</a><o:p></o:p></p></div><p class="MsoNormal"><o:p> </o:p></p></div></div></div></blockquote><blockquote type="cite"><div><span>_______________________________________________</span><br><span>mristudio-users mailing list</span><br><span><a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a></span><br><span><a href="http://lists.mristudio.org/mailman/listinfo/">http://lists.mristudio.org/mailman/listinfo/</a></span><br><span>Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org">mristudio-users-unsubscribe@mristudio.org</a></span><br></div></blockquote></body></html>