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?
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). Here are the bounds in Paraview for the mesh: X range: -98.9 to -9.78 (delta: 89.1) If I put the following for Reflect: plane: X center: 50 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. -Tom On May 17, 2012, at 11:51 AM, Philip A Cook wrote: > 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. > > 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. > > <PastedGraphic-1.png> > > On May 17, 2012, at 10:36 AM, Philip A Cook wrote: > >> Hi, >> >> 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. >> >> 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. >> >> 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. >> >> >> Phil >> >> >> On May 16, 2012, at 11:53 PM, Tom Schoenemann wrote: >> >>> OK, that worked. I've figured out how it works, following what you >>> suggested. >>> >>> 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? >>> >>> -Tom >>> >>> On May 16, 2012, at 5:18 PM, Scott, W Alan wrote: >>> >>>> So, I just tried the following: >>>> *Sources/ Wavelet. Apply. Display this by Outline. >>>> * Filters/ Alphabetical/ Transform. Translate X by 10. Apply. >>>> * Leaving the Transform filter highlighted in the pipeline browser, >>>> Filters/ Common/ Contor. Apply. >>>> * Now, if you turn on visibility of the original Wavelet, you see that the >>>> wavelet has moved along with the contour. >>>> >>>> Or are you saying you want to move the two different files? Then, you use >>>> two transforms – one per file. >>>> >>>> Alan >>>> >>>> From: [email protected] [mailto:[email protected]] >>>> On Behalf Of Tom Schoenemann >>>> Sent: Wednesday, May 16, 2012 2:41 PM >>>> To: Samuel Key >>>> Cc: [email protected] >>>> Subject: [EXTERNAL] Re: [Paraview] different orientation of input files >>>> >>>> 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. >>>> >>>> -Tom >>>> >>>> On May 16, 2012, at 2:32 PM, Samuel Key wrote: >>>> >>>> >>>> Tom, >>>> >>>> Will the Transform filter work for you? (Filters>Alphabetical>Transform) >>>> >>>> It works for me with unstructured meshes. I don't know if it will work >>>> with a surface mesh produced ITK-SNAP. >>>> >>>> Sam Key >>>> >>>> On 5/16/2012 10:29 AM, Tom Schoenemann wrote: >>>> Hi everyone, >>>> >>>> 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. >>>> >>>> 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. >>>> >>>> So Paraview apparently does not read the header info the same way for the >>>> two types of files, even though ITK-SNAP does. >>>> >>>> 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. >>>> >>>> Thanks for any suggestions! >>>> >>>> -Tom >>>> >>>> _________________________________________________ >>>> P. Thomas Schoenemann >>>> >>>> Associate Professor >>>> Department of Anthropology >>>> Indiana University >>>> Bloomington, IN 47405 >>>> Phone: 812-855-8800 >>>> E-mail: [email protected] >>>> >>>> Open Research Scan Archive (ORSA) Co-Director >>>> Consulting Scholar >>>> Museum of Archaeology and Anthropology >>>> University of Pennsylvania >>>> >>>> Homepage: http://mypage.iu.edu/~toms/ >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Please keep messages on-topic and check the ParaView Wiki at: >>>> http://paraview.org/Wiki/ParaView >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://www.paraview.org/mailman/listinfo/paraview >>>> >>>> _________________________________________________ >>>> P. Thomas Schoenemann >>>> >>>> Associate Professor >>>> Department of Anthropology >>>> Indiana University >>>> Bloomington, IN 47405 >>>> Phone: 812-855-8800 >>>> E-mail: [email protected] >>>> >>>> Open Research Scan Archive (ORSA) Co-Director >>>> Consulting Scholar >>>> Museum of Archaeology and Anthropology >>>> University of Pennsylvania >>>> >>>> Homepage: http://mypage.iu.edu/~toms/ >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> _________________________________________________ >>> P. Thomas Schoenemann >>> >>> Associate Professor >>> Department of Anthropology >>> Indiana University >>> Bloomington, IN 47405 >>> Phone: 812-855-8800 >>> E-mail: [email protected] >>> >>> Open Research Scan Archive (ORSA) Co-Director >>> Consulting Scholar >>> Museum of Archaeology and Anthropology >>> University of Pennsylvania >>> >>> Homepage: http://mypage.iu.edu/~toms/ >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Please keep messages on-topic and check the ParaView Wiki at: >>> http://paraview.org/Wiki/ParaView >>> >>> Follow this link to subscribe/unsubscribe: >>> http://www.paraview.org/mailman/listinfo/paraview >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Please keep messages on-topic and check the ParaView Wiki at: >> http://paraview.org/Wiki/ParaView >> >> Follow this link to subscribe/unsubscribe: >> http://www.paraview.org/mailman/listinfo/paraview > _________________________________________________ P. Thomas Schoenemann Associate Professor Department of Anthropology Indiana University Bloomington, IN 47405 Phone: 812-855-8800 E-mail: [email protected] Open Research Scan Archive (ORSA) Co-Director Consulting Scholar Museum of Archaeology and Anthropology University of Pennsylvania Homepage: http://mypage.iu.edu/~toms/
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