<div dir="ltr">Image registration quality is, in the end, judged by our eyeballs.<div>If there was a quantitative measure to judge if it's working or not (regardless of head-to-head or brain-to-brain), we would have used such a measure to achieve the better automated registration.</div>
<div><br></div><div>So, I would say, if the brains are well registered by the head-to-head, there is nothing wrong.</div><div>Head-to-head does fail more than brain-to-brain. So, extra effort for skull-stripping may worth, but as long as the results look decent, head-to-head is fine. When you encounter failure, you could pre-register them by manual landmarks or by skull-stripping. Either way, blind automated processing is always risky.</div>
<div><br></div><div>It also depends on image. DTI data with long echo time tend to suppress non-brain tissue. So the signal is dominated by the brain anyway. T1 has much more intense signals from outside the brain. So, registration may fail more with T1 for head-to-head.</div>
<div><br></div><div>In our atlas, we offer both non-skull-stripped and skull-stripped images.</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, May 26, 2014 at 10:55 AM, 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"><div dir="auto"><div>Thank you Dr. Mori,</div><div>I have followed the manual approach described in <span style="font-family:'.HelveticaNeueUI';font-size:15px;line-height:19px;white-space:nowrap"><a href="http://lists.mristudio.org/pipermail/mristudio-users/2010/001382.html" target="_blank">http://lists.mristudio.org/pipermail/mristudio-users/2010/001382.html</a> </span>and i achieved good skull stripping results. </div>
<div>I understood from your reply that if i do not do skull stripping, the operation will be named head to head registration rather than brain to brain registration and i see that <span style="font-family:AdvTT5843c571;font-size:9pt">ICBM-DTI-81 atlas is skull stripped, isn't it?, My question is if i do not do skull stripping, shall i do registration with another atlas to have more accurate results of brain registration?</span></div>
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<p><span style="font-size:9.000000pt;font-family:'AdvTT5843c571'">Thank you for your kind reply</span></p><p><span style="font-size:9.000000pt;font-family:'AdvTT5843c571'">Shaimaa <br></span></p>
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</div>On May 26, 2014, at 3:12 PM, "Susumu Mori" <<a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr">Hi Shaimaa,<div>
<br></div><div>If you don't skull strip, you are doing head-to-head registration. If you skull-strip, it is brain-to-brain registration.</div><div>You could argue the latter would be more accurate if you are interested in the brain.</div>
<div>However, the latter could be influenced by the quality of the skull-strip and it usually requires manual quality control.</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, May 26, 2014 at 9:19 AM, 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"><div dir="auto"><div style="text-align:left;direction:ltr">Thank you very much, i have an inquiry, should this step be done before normalization to brain atlas, or normalization can be done correctly without this step(skull stripping)?</div>
<div style="text-align:left;direction:ltr"><br></div><div style="text-align:left;direction:ltr">Thanks again </div><span><font color="#888888"><div style="text-align:left;direction:ltr">Shaimaa</div></font></span><div>
<div><div style="text-align:left;direction:ltr"><br></div><div><br>On May 25, 2014, at 9:39 PM, "Dorian P." <<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@gmail.com</a>> wrote:<br><br>
</div><blockquote type="cite"><div><div dir="ltr">Hi Shaimaa,<div><br></div><div>If you did not get help on this, I think skull stripping helps. Those are voxels that we don't really need to have a part in the calculation (and they are not just part of the skull but inferior soft tissues as well).</div>
<div><br></div><div>I used to do skull stripping by coregistering the T1 on FA, running segmentation of T1, and creating a mask of CSF and white matter. Then just multiply the mask with the FA. This can even be done automatically with a batch.</div>
<div><br></div><div>Dorian</div><div>TJU</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-05-22 9:50 GMT-04:00 Shaimaa Abdelsattar <span dir="ltr"><<a href="mailto:shaimaa96@hotmail.com" target="_blank">shaimaa96@hotmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello experts,<br>
Is skull stripping a must do step before doing normalization?, if so, what is its importance and how can it be done?<br>
<br>
Thanks<br>
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