<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-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 class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-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 class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; ">Input</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Image (00000000039FFC80)</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> RTTI typeinfo: class itk::Image<short,3></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> ...</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> LargestPossibleRegion: </span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Dimension: 3</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Index: [0, 0, 0]</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Size: [512, 512, 70]</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> BufferedRegion: </span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Dimension: 3</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Index: [0, 0, 0]</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Size: [512, 512, 70]</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> RequestedRegion: </span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Dimension: 3</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Index: [0, 0, 0]</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Size: [512, 512, 70]</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Spacing: [0.2734, 0.2734, 1.69992]</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Origin: [-135.322, -47.2921, -102.134]</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> Direction: </span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">0.986099 0.164923 -0.0200774</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">-0.165591 0.965578 -0.200612</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">-0.0137026 0.201148 0.979465</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> IndexToPointMatrix: </span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> 0.269599 0.0450899 -0.03413</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">-0.0452726 0.263989 -0.341024</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">-0.00374629 0.0549939 1.66501</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> PointToIndexMatrix: </span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> 3.60681 -0.605614 -0.0501069</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">0.60329 3.53173 0.735726</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">-0.0118108 -0.118012 0.576182</span></font></div></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">"</span></font></div>