[Paraview] combining a voxel-based stat file with a surface mesh?
Tom Schoenemann
toms at indiana.edu
Thu May 24 15:01:58 EDT 2012
Just wondering if anyone had any hints they could give me about things to try.
-Tom
On May 19, 2012, at 10:16 AM, Tom Schoenemann wrote:
> So, how would one "layer" a stat (voxel data) file over a mesh file, to color code the surface of the mesh?
>
> -Tom
>
> On May 18, 2012, at 7:14 PM, Tom Schoenemann wrote:
>
>> I have figured out how to get my surface meshes (from ITK-SNAP) to line up perfectly with my stat data (calculated originally on the same image). Here is how I did it:
>>
>> 1) reflected the ITK-SNAP surface mesh about the X axis:
>> With the surface mesh highlighted in the pipeline browser, select
>> Filters>Alphabetical>Reflect
>> set:
>> Plane: X
>> Center: 0
>> Press "apply"
>>
>> 2) load the stat data file (press "apply")
>> Go to the Information tab for this file and note the X, Y, and Z range bounds for this file. The bounds for my image say, for example:
>> X range: 109 to 218 (delta: 109)
>> Y range: -107 to -0.5 (delta: 106)
>> Z range: 136 to 272 (delta: 136)
>>
>> 3) return to the ITK-SNAP surface mesh, reflected version (click on the "Reflect" object in the pipeline browser listed just below your ITK-SNAP surface mesh file, so that it is highlighted). Then select:
>> Filters>Alphabetical>Transform
>> In the "Translate" boxes of the Transform properties tab, enter the first number for each of your X, Y, and Z ranges, that you noted in step 2 above, in each of the boxes (unfortunately not labeled "X", "Y" and "Z").
>> E.g., for my data, the boxes for the "Translate" row would read:
>> Translate: 109 -107 136
>> Leave the "Rotate" and "Scale" at their default values.
>> Press "apply"
>>
>> This moves the mesh to perfectly overlap my stat data.
>>
>> However, now I can't figure out how to have the stat data attach to my beautiful ITK-SNAP surface mesh. I tried
>> Filters>Alphabetical>Append Attributes
>> with both the translated (and previously reflected) mesh highlighted along with the stat data file, but this doesn't seem to work. The AppendAttributes object now claims to have my stat data attached (Properties shows them as scalars), but there is no option to display them. The "color by" option under the display tab for this object only has "solid color" as an option. Any ideas how I might be able to get these scalars to display on my beautiful mesh?
>>
>> -Tom
>>
>> On May 18, 2012, at 12:38 PM, Tom Schoenemann wrote:
>>
>>> 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: paraview-bounces at paraview.org [mailto:paraview-bounces at paraview.org] On Behalf Of Tom Schoenemann
>>>>>>> Sent: Wednesday, May 16, 2012 2:41 PM
>>>>>>> To: Samuel Key
>>>>>>> Cc: paraview at paraview.org
>>>>>>> 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: toms at indiana.edu
>>>>>>>
>>>>>>> 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: toms at indiana.edu
>>>>>>>
>>>>>>> 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: toms at indiana.edu
>>>>>>
>>>>>> 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: toms at indiana.edu
>>>
>>> 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: toms at indiana.edu
>>
>> 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: toms at indiana.edu
>
> 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: toms at indiana.edu
Open Research Scan Archive (ORSA) Co-Director
Consulting Scholar
Museum of Archaeology and Anthropology
University of Pennsylvania
Homepage: http://mypage.iu.edu/~toms/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.paraview.org/pipermail/paraview/attachments/20120524/ee0d8578/attachment-0001.htm>
More information about the ParaView
mailing list