<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">OK, so Paraview screws up NIFTI coordinates, or doesn't read the header right? The surface mesh that ITK-SNAP makes is in vtk format, so it must be that ITK-SNAP doesn't put the orientation info into the right format? <div><br></div><div>Looking closely at my image, I can see that the vtk mesh in Paraview is indeed left-right reversed compared to the original in ITK-SNAP (in addition to being shifted in various ways out of alignment inexplicably). </div><div><br></div><div>Here are the bounds in Paraview for the mesh:</div><div><br></div><div>X range: -98.9 to -9.78 (delta: 89.1)</div><div><br></div><div>If I put the following for Reflect:</div><div>plane: X</div><div>center: 50</div><div><br></div><div>Then the images are no longer left-right reversed from each other, but they are still not overlapping. There is some kind of Y and Z shift also going on.</div><div><br></div><div>-Tom</div><div><br></div><div><br><div><div>On May 17, 2012, at 11:51 AM, Philip A Cook wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Trying this out on some actual data - it seems the reflection should actually be about the boundary of the image, not the center. Here the x-bounds of my image are 114 to 337 in Paraview (note this does not agree with the NIFTI or ITK coordinates), so I reflected the mesh (blue) about 114 in the x-axis, giving me what I think is a correctly oriented mesh. <br><br>Unfortunately, there appear to be other transformations at play as well. You can't see it in this view but the red mesh is offset in the Z-axis. I think this is because of the disagreement between the NIFTI and Paraview coordinates.<br><br><span><PastedGraphic-1.png></span><br><br>On May 17, 2012, at 10:36 AM, Philip A Cook wrote:<br><br><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I have had some success with the Reflect filter. Often the SNAP meshes are reflected about the origin of the image. Thus I do Reflect on the mesh (I always find it easier to transform the mesh rather than the image in Paraview), with Plane set to X / Y / Z as appropriate, and Center set to the Center of the image. <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The Center of the image in Paraview might not agree with what's in the image header, at least not for NIFTI files. You can figure out the Center in Paraview by selecting the image and then looking at the Information tab. The Bounds box will tell you the min and max in each coordinate. For the Reflect filter, you want the Center to be halfway between the min and max bound of the image.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">This usually solves my problems with meshes and images not lining up. I'm assuming here that you are loading the same image from which the mesh was defined.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Phil<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On May 16, 2012, at 11:53 PM, Tom Schoenemann wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">OK, that worked. I've figured out how it works, following what you suggested.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Unfortunately, Paraview didn't just shift the data over, leaving it in the same orientation, it also inexplicably changed the orientation by several degrees (??). Even if I am able to get the two boxes in basically the same location, the shifted orientation makes it impossible to be confident the data are overlaid in the right places. This is very frustrating. Apparently Paraview makes random changes to the orientation?? Why on earth would it do that?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-Tom<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">On May 16, 2012, at 5:18 PM, Scott, W Alan wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">So, I just tried the following:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">*Sources/ Wavelet. Apply. Display this by Outline.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Filters/ Alphabetical/ Transform. Translate X by 10. Apply.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Leaving the Transform filter highlighted in the pipeline browser, Filters/ Common/ Contor. Apply.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">* Now, if you turn on visibility of the original Wavelet, you see that the wavelet has moved along with the contour.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Or are you saying you want to move the two different files? Then, you use two transforms – one per file.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Alan<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">From: <a href="mailto:paraview-bounces@paraview.org">paraview-bounces@paraview.org</a> [mailto:paraview-bounces@paraview.org] On Behalf Of Tom Schoenemann<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Sent: Wednesday, May 16, 2012 2:41 PM<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">To: Samuel Key<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Cc: <a href="mailto:paraview@paraview.org">paraview@paraview.org</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Subject: [EXTERNAL] Re: [Paraview] different orientation of input files<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I must be missing something. It only seems to move the bounding box, but not the location of the contour itself.. Not sure what that would be useful for, but in any case, I need to move the contour and/or data within the workspace, so the two overlap. Transform is only changing the box, not changing the location of the object within the box. Again, maybe I'm missing something.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">-Tom<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On May 16, 2012, at 2:32 PM, Samuel Key wrote:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Tom,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Will the Transform filter work for you? (Filters>Alphabetical>Transform)<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">It works for me with unstructured meshes. I don't know if it will work with a surface mesh produced ITK-SNAP.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Sam Key<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On 5/16/2012 10:29 AM, Tom Schoenemann wrote:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi everyone,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I have a question about changing/editing the orientation and origin information about an input file. Basically, the problem is this: I have a 3D volume (originally voxel data) file that contains statistics on its surface that I want to display color-coded. I can create a nice smoothed version of the surface using a different piece of software (ITK-SNAP), and this is the surface I'd like to use to display my stats (Paraview does not allow you to smooth the surface in the same way that ITK-SNAP does, eliminating the stair-step surface artifacts). I can indeed read both the stats file and the surface file from ITK-SNAP into Paraview, but unfortunately they now have different origins. That is, they don't overlap (the bounding box for the stats is completely outside the surface model that ITK-SNAP created.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Originally, both files had the same orientation and origin: ITK-SNAP used the same file to create the beautiful surface that the stats were created with. <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">So Paraview apparently does not read the header info the same way for the two types of files, even though ITK-SNAP does. <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Is there a way to change the origin and/or orientation of files in Paraview? I'm assuming there is a simple transform I could figure out by trial and error to get them to overlap again, but I don't know how or where I would do this.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Thanks for any suggestions!<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">-Tom<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">_________________________________________________<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">P. 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-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><span class="Apple-style-span" style="font-size: 12px; "><div>_________________________________________________</div><div>P. Thomas Schoenemann</div><div><br class="khtml-block-placeholder"></div><div><div>Associate Professor</div><div>Department of Anthropology</div><div>Indiana University</div><div>Bloomington, IN 47405</div><div>Phone: 812-855-8800</div><div>E-mail: <a href="mailto:toms@indiana.edu" style="text-decoration: none; ">toms@indiana.edu</a></div></div><div><br></div><div>Open Research Scan Archive (ORSA) Co-Director</div><div>Consulting Scholar</div><div>Museum of Archaeology and Anthropology</div><div>University of Pennsylvania</div><div><br></div><div><div>Homepage: <a href="http://mypage.iu.edu/~toms/">http://mypage.iu.edu/~toms/</a></div><div><br></div></div></span></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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