Hi, Thanks alot for your response, Ken. Herewith,pls see the attachment: how the 3 small masks are looked like. So the large mask(it's not seen here) encompass all three masks. All 4 masks are saved in different folders and all of them have been called in, stacked together and converted to vtk to call into Paraview. So how should i move forward in order to make visible the small 3 masks in the model? Let me know anyone of your thoughts about it. -- Warm regards, Chathuri Gunasekera.
On Wed, May 11, 2016 at 7:12 PM, Moreland, Kenneth <[email protected]> wrote: > Chathuri Gunasekera, > > > > Are your patches available as fields in the data? If so, you should be > able to use the Threshold filter with the patches to remove the holes. > > > > -Ken > > > > *From: *Chathuri Gunasekera <[email protected]> > *Date: *Tuesday, May 10, 2016 at 8:31 PM > *To: *Kenneth Moreland <[email protected]> > *Cc: *"[email protected]" <[email protected]> > *Subject: *[EXTERNAL] Re: [Paraview] [ParaView] How to add thickness to > each slice when generating a 3D model > > > > Hi to all, > > > > @ Ken, thank you so much for your response. Really admire it. > > > > 1. Yes, i am 100% certain that all the masks are called in. > > But let me be more into detail. > > Basically, i have: 1 big mask and 3 patches (which are also saved as > masks). Sorry Ken, i think i should have use patch instead of hole [ this > patch eventually represent some special features{but these features > eventually build up as tubes when it comes to a 3D model.} in a human organ > as i am trying to model a human organ itself ]. ANyhow, i am sorry if i > make you confuse. > > > > You're right Ken, most of the stuff is done in MatLab but all the work > looks error-free(because it works fine atleast in MatLab). But i am skeptic > of one thing. Should i have to have a transparent big mask in order to see > the 3 patches inside the big mask? Is that why , i don't see the patches ? > Kindly guide me. > > > > 2. I will try that out too. > > > > Anyhow, thank you so much for your detailed response Ken. That is a great > help. > > > > > > -- > > Warm regards, > > Chathuri Gunasekera. > > > > > > > > > > On Wed, May 11, 2016 at 12:08 AM, Moreland, Kenneth <[email protected]> > wrote: > > Chathuri Gunasekera, > > > > (Responding back to ParaView list to allow others to see and comment.) > > > > 1. I’m not sure why you are not see the 3 holes you expect in your mask. > It looks like most of your process is building the data in MATLAB. Perhaps > something is going wrong there. ParaView must be recognizing the mask since > the region outside of the external boundary is removed. Are you sure your > three holds are represented in the mask? > > > > 2. It sounds like you are finding the mask boundary in a slice. A slice is > by definition contained in a 2D plane. You can restore the 2mm thickness > manually by running the Extract Surface filter and then the Linear > Extrusion filter. > > > > -Ken > > > > *From: *Chathuri Gunasekera <[email protected]> > *Date: *Tuesday, May 10, 2016 at 12:03 PM > *To: *Kenneth Moreland <[email protected]> > > > *Subject: *[EXTERNAL] Re: [Paraview] [ParaView] How to add thickness to > each slice when generating a 3D model > > > > Hi Ken, > > > > Your detailed description is very much appreciated. Thank you so much. > > > > Kindly note that following is what i have done in MatLab : > > a. Segmented images as Masks (just x,y cordinates) > > b. Saved as a .mat file > > c. Then append z coordinate( z coordinate is the slice thickness which, > each slice has a thickness of 2mm) to the above said mask. Hence, now the > image is 3D (saved as .mat file) > > d. Convert the 3D image into real world coordinates . So x,y,z all are in > mm now. (saved as .mat file) > > e. Since i have about 8 sets and about 50 images per set. Then find the > smallest dimension for a particular set. > > f. Crop the image (saved as .mat file) > > g. Stack the image (saved as .mat file) > > h. Finally convert the .mat file to .vtk file > > i. Then open the .vtk files in Paraview > > Let me send you 2 outputs which i have obtained so far > > > > 1. segmented masked images. I prefer this method because this image looks > close to my expectation(i expect a 3D model). Also i have 3 more masks > which represent 3 more features inside the big mask (meaning i expect 3 > holes inside the big image). But i simply cannot see the 3 holes inside > this big mask. What mistake i am doing here? Why can't i see the 3 holes > inside the big mask. > > > > 2. segmented masked --> converted RGB image to binary and then find the > boundary of the mask. So the reason for why i asked the thickness is that > for this output i can't see the 2mm thickness . > > > > Kindly note that in order to obtain above output i have used couple of > masks(slices) and stacked them together. > > > > Your assistance is really appreciated here as i was struggling to get a > proper 3D model for sometime now and all my efforts are not succeeded yet. > > > > Thank you. > > > > -- > > Warm regards, > > Chathuri Gunasekera. > > > > > > > > On Tue, May 10, 2016 at 9:50 PM, Moreland, Kenneth <[email protected]> > wrote: > > I think we need more information before we can answer your questions. > > > > Your first question was how to “add thickness” to image slices. If you > have image slices, you usually want to load them in as a 3D stack and treat > them like a volume. The spacing between the slices is typically specified > by the data file itself or by an option in the reader (of which there are > almost 100 different types in ParaView). So how you do that depends on your > data format. > > > > You simply said that your data comes from MATLAB. That’s not very > specific, since it is possible to output lots of different types of files > from MATLAB. If you are not doing it yet, you might consider this MATLAB > module that writes out VTK files (which ParaView handles very well): > http://www.mathworks.com/matlabcentral/fileexchange/47814-export-3d-data-to-paraview-in-vtk-legacy-file-format > . I haven’t used it myself (I use MATLAB very infrequently), but it looks > pretty full featured. You might want to check that out. > > > > You also mentioned that the image segmentation is represented by masks. > The easiest way to deal with that is probably to use the Threshold filter > to remove all cells that are masked out. > > > > -Ken > > > > > > *From: *ParaView <[email protected]> on behalf of Chathuri > Gunasekera <[email protected]> > *Date: *Tuesday, May 10, 2016 at 4:49 AM > *To: *ParaView <[email protected]> > *Subject: *[EXTERNAL] Re: [Paraview] [ParaView] How to add thickness to > each slice when generating a 3D model > > > > Also,i need to mention that segmented images are saved as Masks. > > > > Kindly tell me, when using Paraview software should i have to use the > boundary or the mask of the segmented image for the purpose of building a > 3D model. (kindly correct me, if i am wrong as i am new to Paraview) > > > > Hope to hear from you soon. > > > > Thank you. > > > > On Tue, May 10, 2016 at 2:53 PM, Chathuri Gunasekera <[email protected]> > wrote: > > Hello everyone, > > > > My goal is to generate a 3D model of human organ. > > > > Suppose i have segmented images in each set(each slice is saved using > MatLab software). > > > > So i want to know what are the options which paraview have in order to add > the thickness to each slice. > > > > Your feedback is appreciated. > > > > > > > > -- > > Warm regards, > > Chathuri Gunasekera. > > > > > > -- > > Warm regards, > > Chathuri Gunasekera. > > > > > > > > > > > > >
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