<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div style="text-align: left;direction: ltr; ">Hello experts,</div><div style="text-align: left;direction: ltr; ">I've got confused. Please revise with me the steps i followed to find where was the mistake.</div><div style="text-align: left;direction: ltr; ">1.First i uploaded my philips dicom data and transformed it to rec files.</div><div style="text-align: left;direction: ltr; ">2. Then i applied AIR in Dti studio using affine transformation, then I save the resulting image as .rec file again</div><div style="text-align: left;direction: ltr; ">3. I performed tensor calculations in dti mapping, and i saved FA file.</div><div style="text-align: left;direction: ltr; ">4. I coregistered fa with <span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">ICBM_DTI_81 FA map in diffeomap again choosing affine. </span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">5. I opened the updated fa in Roi editor and then i opened wmpm 90%</span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">6. I found some rois were perfectly matched and others were larger than the anatomical areas</span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; "><br></span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">My images were 144* 144</span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">And fov were 230 * 230</span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">Slice thickness 2</span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">Image blocks 1</span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">Nex 1</span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">Image slices 70</span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; "><br></span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">Please tell my how can i adjust the roi file over my anatomical areas</span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; "><br></span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">Sorry for taking your time and thank you for your concern</span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; "><br></span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">Thanks</span></div><div style="text-align: left;direction: ltr; "><span style="font-family: '.HelveticaNeueUI'; font-size: 15px; line-height: 19px; white-space: nowrap; -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: none; ">Shaimaa</span></div><div style="text-align: left;direction: ltr; "><br></div><div><br>On Nov 15, 2013, at 5:42 PM, "Hangyi Jiang" <<a href="mailto:hjiang@jhmi.edu">hjiang@jhmi.edu</a>> wrote:<br><br></div><div><span></span></div><blockquote type="cite"><div>
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we usually do AIR before Deffiomap, not after,<br>
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hangyi<br>
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<div style="direction: ltr;" id="divRpF441069"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Shaimaa Abdelsattar [<a href="mailto:shaimaa96@hotmail.com">shaimaa96@hotmail.com</a>]<br>
<b>Sent:</b> Friday, November 15, 2013 10:46 AM<br>
<b>To:</b> Hangyi Jiang<br>
<b>Subject:</b> Re: [Mristudio-users] ICBM_DTI_81 image registration<br>
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<div>So after i do registration in deffiomap program, i should perform Air in dti studio </div>
<div>My question was about image registration using <span style="font-family:'.HelveticaNeueUI'; font-size:15px; line-height:19px; white-space:nowrap">ICBM_DTI_81 atlas</span></div>
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I have question about image registration. I have used ICBM_DTI_81 atlas for image registration in my case, control clinical research using linear transformation. After doing this i found good registration after i tested structures by the landmark option. Yet
when i applied their ROI file (WMPM 90%) on my data, I found that the ROIs in the atlas are larger than the actual size of structures of my patients. Is there any solution for this?</blockquote>
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On Nov 15, 2013, at 5:34 PM, "Hangyi Jiang" <<a href="mailto:hjiang@jhmi.edu" target="_blank">hjiang@jhmi.edu</a>> wrote:<br>
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when you do AIR using DtiStudio. the AIR parameter dialog shows two options:<br>
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Rigid Body, this is a 6 parameters transformation method. (or 6 mode as some one said, not strictly);<br>
Affine, this is 12 parameters method (or 12 mode..)<br>
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there is no separate 9 mode selection. it is already included in 12 mode.<br>
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hangyi<br>
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<div id="divRpF225634" style="direction:ltr"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Shaimaa Abdelsattar [<a href="mailto:shaimaa96@hotmail.com" target="_blank">shaimaa96@hotmail.com</a>]<br>
<b>Sent:</b> Friday, November 15, 2013 10:33 AM<br>
<b>To:</b> Hangyi Jiang<br>
<b>Subject:</b> Re: [Mristudio-users] ICBM_DTI_81 image registration<br>
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<div>Thank you,</div>
<div>Where can i find the option to choose 9 or 12 mode to adjust my transformation</div>
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<div>Thanks again</div>
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On Nov 15, 2013, at 3:41 PM, "Hangyi Jiang" <<a href="mailto:hjiang@jhmi.edu" target="_blank">hjiang@jhmi.edu</a>> wrote:<br>
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affine transformation includes scaling.<br>
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hangyi<br>
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<div id="divRpF501603" style="direction:ltr"><font color="#000000" face="Tahoma" size="2"><b>From:</b>
<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">mristudio-users-bounces@mristudio.org</a>] on behalf of Shaimaa Abdelsattar
[<a href="mailto:shaimaa96@hotmail.com" target="_blank">shaimaa96@hotmail.com</a>]<br>
<b>Sent:</b> Friday, November 15, 2013 5:03 AM<br>
<b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
<b>Subject:</b> Re: [Mristudio-users] ICBM_DTI_81 image registration<br>
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<div style="text-align:left; direction:ltr">Hello Dr.Mori, </div>
<div style="text-align:left; direction:ltr">I tried affine transformation and trilinear interpolation</div>
<div style="text-align:left; direction:ltr">How can i include scaling in my linear transformation ? </div>
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<div style="text-align:left; direction:ltr">Thanks</div>
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On Nov 14, 2013, at 4:10 PM, "Susumu Mori" <<a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a>> wrote:<br>
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<div dir="ltr">Hi Shaimaa,
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<div>When you apply the linear registration, did you use 9 or 12-mode, which includes scaling?</div>
<div>ICBM-152 template brain is larger than many subjects. So, your linear transformation better include scaling. </div>
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<div>Usually the parcellation map superimpose pretty well.</div>
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<div class="gmail_quote">On Wed, Nov 13, 2013 at 2:38 PM, Shaimaa Abdelsattar <span dir="ltr">
<<a href="mailto:shaimaa96@hotmail.com" target="_blank">shaimaa96@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
Hi experts,<br>
I have question about image registration. I have used ICBM_DTI_81 atlas for image registration in my case, control clinical research using linear transformation. After doing this i found good registration after i tested structures by the landmark option. Yet
when i applied their ROI file (WMPM 90%) on my data, I found that the ROIs in the atlas are larger than the actual size of structures of my patients. Is there any solution for this?<br>
<br>
Or i should use other atlas for my registration<br>
<br>
Thanks<br>
Shaimaa<br>
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