<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Hi!</span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"> </span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">I have registered two MRIs. The registration pipeline is first rigid and then affine, and the results are ok.
</span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB"> </span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">But now I would try to register only the gray matter of these two images, because I am only interested in the registration of the cortex. So, I have segmented the 2 images and now I am trying to do the same registration (rigid and affine) with two binary MRIs and with the same program and parameters.
</span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB"> </span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">The problem is that now I get the output image all white.
</span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB"> </span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">First I thought it was only problem of the writer of the output image (the interpolation of the resample filter or something like that, due to the output is a binary image too), but I have applied the same transformation (the one obtained from the registration of two gray matters) to a MRI and the transformation is bad done. So, I think it is problem of the registration…
</span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB"> </span></p>
<div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">So, some idea about the problem??
</span></div>
<div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB"></span> </div>
<div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB"></span><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-fareast-font-family: Arial; mso-ansi-language: EN-GB">
<span style="mso-list: Ignore">1)<font face="Times New Roman"> </font></span></span><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">I have to change some parameters or the interpolation or…?
</span></div>
<div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB"></span><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-fareast-font-family: Arial; mso-ansi-language: EN-GB">
<span style="mso-list: Ignore">2)<span style="FONT: 7pt 'Times New Roman'"> </span></span></span><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">Which differences I have to think about to readapt the program?
</span></div>
<div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB"></span><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-fareast-font-family: Arial; mso-ansi-language: EN-GB">
<span style="mso-list: Ignore">3)<span style="FONT: 7pt 'Times New Roman'"> </span></span></span><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">Or some idea to register ok the gray matter?
</span></div>
<div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB"></span> </div>
<div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; mso-pagination: none; mso-layout-grid-align: none"><span lang="EN-GB" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-GB">Thank you!!</span></div>