<br>Never mind, I fixed the problem.<div><br></div><div>Taru<br><div class="gmail_quote">On Fri, Mar 18, 2011 at 10:11 AM, Taru S <span dir="ltr"><<a href="mailto:twrkmail@gmail.com">twrkmail@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><font face="arial, sans-serif"><span style="border-collapse:collapse">Hello,</span></font><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">
<br></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">I am new to ITK and need your help with my MR orientation. I have generated a surface model by segmenting an MR volume generated using ITK from Axial MR dicom slices. </div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">However, when I view the Axial dicom slices they are not correctly oriented (please see the attachment). The sagittal and coronal views in the figure are generated from axial reslicing. As a result of this mis-orientation, the surface model doesn't appear aligned with the slices. </span></font></div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">The direction cosines of my MR dicoms are not orthogonal/identity matrix. The output after applying these direction cosines to my input dicom (Resample image filter )set doesn't seem to make any difference. </div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">Using identity matrix in place of the direction cosines yields black images. I am confused because the images don't appear tilted when viewed using Snap even with Oblique orientation mode.</div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">I will really appreciate your help in resolving this issue.</div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">Thank you,</div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">
Taru</div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">Below is some of the information regarding my input MR dicoms:</div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">"</div><div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">Input</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse">Image (00000000039FFC80)</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> RTTI typeinfo: class itk::Image<short,3></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"> ...</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> LargestPossibleRegion: </span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Dimension: 3</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Index: [0, 0, 0]</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Size: [512, 512, 70]</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> BufferedRegion: </span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Dimension: 3</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Index: [0, 0, 0]</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Size: [512, 512, 70]</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> RequestedRegion: </span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Dimension: 3</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Index: [0, 0, 0]</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Size: [512, 512, 70]</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Spacing: [0.2734, 0.2734, 1.69992]</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Origin: [-135.322, -47.2921, -102.134]</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> Direction: </span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse">0.986099 0.164923 -0.0200774</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">-0.165591 0.965578 -0.200612</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse">-0.0137026 0.201148 0.979465</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br>
</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> IndexToPointMatrix: </span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> 0.269599 0.0450899 -0.03413</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse">-0.0452726 0.263989 -0.341024</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">-0.00374629 0.0549939 1.66501</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br></span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"> PointToIndexMatrix: </span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"> 3.60681 -0.605614 -0.0501069</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">0.60329 3.53173 0.735726</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse">-0.0118108 -0.118012 0.576182</span></font></div></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">"</span></font></div>
</blockquote></div><br></div>