I have sets of .dcm files of an MRI scan. I am trying to convert them into 3d formats like obj (preferably) or fbx to import them into Unity 3d. I used the following open source software dcmtk to convert .dcm file into text file.
Converting DICOM files to text files
However, the dcm files lack the needed information. Is it even possible to convert .dcm files to obj and fbx. if so, could you suggest something?
Thanks
(Edit)
I would like to put my question more precisely: I want to visualize MRI data as a 3D model in Unity 3d. This is possible only when I it stored as .obj or .fbx format. Which format of MRI medical data should I start with to convert to these formats?
Thanks
According to your previous comments you are looking for the necessary information in order to obtain the geometrical information of a DICOM series representing volumetric information (RM, TC, PET, ...)
In this case, you should have a look at the Roni Zaharia web site where he explains very clearly the concepts related to orientation and geometry of the DICOM images: DICOM is easy: Getting oriented
In this particular page you will find information about Pixel Spacing, Image Orientation, Image Position, Slice Thickness, and Slice Location, as well as additional information references.
Related
I need to display the DICOM images in a browser. This requires, the DICOM to be converted to PNG (or any other compatible) format.
I also need to calculate some overlay pixels based on dynamic input from the user. On conversion to PNG, I am getting 4 values (Alpha, R, G, B). But I can not use these values for my calculations. I need the original HU values from the DICOM images.
Is there any way that, PNG can contain the original DICOM values. I heard that using monochromatic 16 bit PNG format it is possible. How do we do that?
Alternatively, how to load DICOM pixel data in browser preserving HU values?
When you convert DICOM pixel data to other non-DICOM format like PNG, BMP, JPG, J2K etc., the data you are looking for is lost. You may further research for TIF format whether it preserves the data and it loads in browser. I guess it will not.
I will recommend to avoid this way. Instead, I will suggest using DICOM pixel data as-is in browser. This can be achieved by involving some java-script DICOM toolkit for browsers like cornerstone. You may also look for other toolkit if available and suits you.
Note that this involves learning curve. It will be too broad here to explain its working.
I want to display a 3D bathymetry data in paraview, the file datatype is netcdf:
it has two dimensions and three variables;
my netcdf file format
When I try to open it in paraview: it is a 2D not 3D,
2D
I want to display Dlike this:
3D
i’m sorry for bad English and less infomation.
The most simple way to do that is to use the Extrusion Surface representation.
https://blog.kitware.com/a-new-embossing-representations-plugin-for-paraview/
Open ParaView
Tools -> Manage Plugins -> Embossing Representations
Create a new view
Open your file
Switch representation to Extrusion Surface
Only Available since ParaView 5.6.0. Keep in mind this is only a representation, not a change to the actual data. If you want to change the data, you will have to use CellDataToPointData and WarpByScalar, which will require more tweaking.
I have a series of dicom images and did change the HUs in the images using MATLAB scripts, then I imported them in ImageJ for display. Then I realised I can modify the images using ImageJ gui (which much easier, just moving the mouse). However, when I saved the modified images in ImageJ, they were saved in tiff format.
My question is that, is there a way to save images in imageJ as dicom format ?
or is there away to convert tiff format to dicom using MATLAB ?
Any suggestion ?
You can convert tiff format to dicom with dicomwrite:
dicomwrite( imread('input_image.tif'), 'output_image.dcm')
The following plugins allow writing DICOM files directly from ImageJ:
DICOM Import and Export plugins
The Tudor DICOM Tools
How the line smoothness in a contour plot can be improved for publications? For instance, the dotted lines look really bad, the continuous lines look as if their thickness varies. See below
Here's part of the code:
Vals = [0:5:200]; contourf(X,Y,W,Vals,'EdgeColor','k','LineWidth',1.2,'LineStyle',':');axis square;grid;hold on
Vals = [10:10:200]; contour(X,Y,W,Vals,'EdgeColor','k','LineWidth',1.2);
Vals = [20 : 20 : 200]; [C,h] = contour(X,Y,W,Vals,'Color','k','LineWidth',1.8);
clabel(C,h,'FontName','Palatino Linotype','FontAngle','italic','Fontsize',9,'Color','w')
print -djpeg -r300 filename
Thanks!
Saved as png doesn't help much... check the lines :/ See below:
Check the dotted lines now...
Here's saving as eps (-r1200)... it looks better
Exporting as vector graphics will definitely improve the image over what you see on your screen; I use LaTeX for publications and you can either export to eps for postscript output, and use epstopdf for PDF output, and embed these directly in your document; that would be the best solution.
Additionally, there are also a bunch of general utilities for making your plots look better for camera-ready publications, the most notable that comes to mind is exportfig, which has a load of features to help even with pixel graphics. These go above and beyond just generating smoother-looking images.
http://www.mathworks.us/matlabcentral/fileexchange/23629-exportfig
(copied from that page):
This function saves a figure or single axes to one or more vector and/or bitmap file formats, and/or outputs a rasterized version to the workspace, with the following properties:
Figure/axes reproduced as it appears on screen
Cropped borders (optional)
Embedded fonts (pdf only)
Improved line and grid line styles
Anti-aliased graphics (bitmap formats)
Render images at native resolution (optional for bitmap formats)
Transparent background supported (pdf, eps, png)
Semi-transparent patch objects supported (png only)
RGB, CMYK or grayscale output (CMYK only with pdf, eps, tiff)
Variable image compression, including lossless (pdf, eps, jpg)
Optionally append to file (pdf, tiff)
Vector formats: pdf, eps
Bitmap formats: png, tiff, jpg, bmp, export to workspace
This function is especially suited to exporting figures for use in publications and presentations, because of the high quality and portability of media produced.
Update: I see your example code now. Did you try changing -r300 to some really high value? More pixels per inch should make everything look smoother. For publication, crank it up really high, like -r1200.
Original:
One thing you can try is exporting the plot in some format that supports vector graphics. Matlab supports both PDF and EMF, so try one of those. Export using the saveas command or from the figure's "File -> Save as" menu item. After that, open or import the image file in some other application and hopefully it will look better.
Please add a new screenshot if you get a nicer image!
quick question: I'm creating "random" polygons using either the patch() or the fill() function in Matlab. This works quite good and it is plotted correctly.
However, I need to at least save a few hundres polygons as images to my hard drive for working with them later - so I'm looking for a way to directly save the image in my function rather than saving each polygon myself using the file-menu.
Is there any way to do this?
Thanks in advance!
You can indeed use the print function, but I would not use the jpeg device. JPEG is never the right format for plots (you will get a lot of artifacts near all your lines).
If you need a bitmap image, try the png or tiff device. If you don't need a bitmap, use the appropriate vector image format: fig is the native MATLAB format (which allows you to edit the plot afterwards), so this is the best one if you stick with MATLAB for all your operations. For exporting to other software, I would recommend pdf (works almost anywhere), epsc (EPS with color, great for LaTeX or inkscape), wmf/emf (Windows Metafile, so Windows only, but great for including the images in MS Office). Or you could of course use any of the other formats mentioned in the print documentation.
Sometimes it's a pain in the neck to get the format of your image all right (especially with PDF output). Just take a look at the different properties of your figure and more specifically the PaperSize, PaperUnits and PaperPosition.
The easiest way, and I guess the best solution, is to save as a .fig file. You can do this by using saveas:
h = figure;
% your plot commands here
saveas(h,'mFile.fig');
Afterwards, you can reload the image with the openfig function:
openfig('mFile.fig');
Have to add this answer. This function is helping a lot.
This function saves a figure or single axes to one or more vector and/or bitmap file formats, and/or outputs a rasterized version to the workspace, with the following properties:
- Figure/axes reproduced as it appears on screen
- Cropped/padded borders (optional)
- Embedded fonts (pdf only)
- Improved line and grid line styles
- Anti-aliased graphics (bitmap formats)
- Render images at native resolution (optional for bitmap formats)
- Transparent background supported (pdf, eps, png)
- Semi-transparent patch objects supported (png only)
- RGB, CMYK or grayscale output (CMYK only with pdf, eps, tiff)
- Variable image compression, including lossless (pdf, eps, jpg)
- Optionally append to file (pdf, tiff)
- Vector formats: pdf, eps
- Bitmap formats: png, tiff, jpg, bmp, export to workspace