Disclaimer: I am not a medical guy and I don't deal with volumes very often.
I suspect that your best bet is to use ITK (or VTK) filters to somehow create one or more axis-aligned, non-overlapping volumes out of the original data. This could be done as a pre-processing step or within the reader. I don't know which filters would be best for this. I suspect that you will need at least vtkImageReslice. You might need to go to the ITK or VTK list for more detail. Once you have non-overlapping, axis-aligned volumes, you can volume render them the usual way. It would be pretty easy to write a volume representation that can handle a multi-block dataset of non-overlapping images. Best, -berk On Wed, May 23, 2012 at 3:38 AM, Christoffer Green < [email protected]> wrote: > Hello > > Thank you for the suggestions. > > The use case is that I am currently writing an application (based on > ParaView) that is going to be used by doctors/researchers for visualizing > MRI data of blood flow (some more information can be found here: > http://www.jcmr-online.com/content/14/S1/W14 ). This means that the user > has some data files (volumes of velocity data, 2d image planes, none of the > data is axis aligned, all of it overlapping) and they need to get this data > in to the application and I am currently trying to figure out what the > recommended way of doing this would be. I can not rely on the users having > any deep knowledge of ParaView, 3d math or even above basic general > computer skills so asking them to write macros or manually rotating the > data might not work well :) > > The data->cleantogrid->volume render workflow sounds interesting. My > current problem with it (as well as using mergeblocks instead of > cleantogird) is that it appears to take about 8 hours to produce a result > that way (I do not know what that result is yet since I have not seen it > through to the end). This is off course unacceptably slow but perhaps this > is a bug? > > But if I understand you correctly you are saying that unstructured grid > is the data format that would be best for this. Is there any file format > that when imported is an unstructured grid by default and would doing it > that way speed things up massively? > > BR/ Christoffer > > > On Tue, May 22, 2012 at 3:39 PM, Berk Geveci <[email protected]>wrote: > >> What is your end goal? Volume rendering a collection of MRI volumes >> (together? non-overlapping?) that may not be axis aligned? One way of doing >> this in ParaView would be to convert them to unstructured grid (by using >> clean-to-grid for example) but this comes at a large memory overhead and >> performance overhead. The simpler and more efficient way of doing it is to >> load each MRI volume as a separate image data and then use the >> Transformation setting from the Display panel to position and orient them >> as necessary. It would pretty straightforward to write a macro to do all of >> this automatically given a particular file. >> >> On Mon, May 21, 2012 at 7:57 AM, Christoffer Green < >> [email protected]> wrote: >> >>> Hello >>> >>> What are your thoughts on the best file format to use when doing volume >>> rendering in ParaView? >>> >>> I have been trying out the ensight format and the vtk format and find >>> them less then ideal, is there anything better? >>> >>> Findings for ensight: >>> ParaView does not appear to support volume rendering of ensight files >>> due to it not supporting volume rendering of multi-block datasets and the >>> ensight reader always imports things in multi block mode. There are ways to >>> get around this (tetrahedralize together with calculator filter) but the >>> end results appear to be extremely slow when volume rendering. >>> >>> Findings for vtk: >>> Importing a volume of data as image data and volume rendering it works >>> well but image data in the vtk format must always be aligned to the global >>> orthogonal (x, y, z) axes so it cannot be rotated. Since we have multiple >>> data files that all must be positioned and rotated in a scene (MRI volumes >>> and image planes) this makes things uncomfortable. There is a transform >>> filter in ParaView but after applying it to image data it changes the data >>> type to curvalinear grid which ParaView cannot volume render. >>> >>> >>> What are the alternatives? >>> >>> BR/ Christoffer >>> >>> _______________________________________________ >>> 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 >>> >>> >> >
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