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using MRI data


puma.snyder

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I wonder what's the best approach for reconstructing geometry from mri data.

For now I assume that I will somehow have to use the isosurface sop, but maybe

there are also different approaches possible. Has someone done this before

and could guide me in the right direction?

Will the upcoming level sets be helping in such a case?

Thanks a lot guys :D

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You could generate a .geo from it and then run i3dconvert to convert it into an .i3d file which you can then either render it directly via a VEX 3D Texture Fog SHOP or convert it into a surface using the 3D Texture mode of the IsoSurface SOP.

To see how the .geo file looks like, you could render out an example i3d file using a 3D Texture Generator ROP with a default VEX Fluffy Cloud SHOP. Then use i3dconvert to convert it from .i3d to .geo. Basically, it's a just a regular 3D grid of points with the attribute density store at each point.

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Thank you Edward

I understand the second part but I have no idea how I can create the initial .geo from the mri. Could you maybe give me some advice for this step as well?

Any ideas about the level set question? When I did a google search on mri and level stes there where many results, so I guess I will be helpfull, but for now my understanding of level are still very limited, so I'm not sure how to use them in such a case.

Thanks again

Achim

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Its hard to say how to convert MRI data because you need to know what format the data is in in the first place. Is it some kind of voxel format? Are they cubes or "stretched" in depth? Is the data binary or ascii (text)? Or image slices? Are they evenly spaced slices?

There is often a little bit of simple reverse engineering for this first step - perhaps a very simple script in maybe PERL to strip out the data and dump it into a the simple GEO format file. Do you have an MRI data file for us to look at?

Cheers,

Jason

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Very often medical mri data files are only raw data written out. They even don't contain the resolution of the dataset or the datatype used (floats, bytes, etc.). Most often these informations are then specified in the filename (like data_description_256x256x128.raw or something similar)

There are other formats (e.g. dicom), but I never had a huge interrest in medical visualization, so I can't really comment on that one.

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If you hunt around on the web you will find lots of free tools for viewing mri data. We've done a ton of stuff with it but we have our own marching cubes software that reads it in as raw. Depending on the exact format you can also sometimes open it in photoshop as raw, but you need to know the exact size. Usually 512 x 512 but not always.....

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Hey Jason

For now I want to test this with one of the files found here:

ftp://ftp.nlm.nih.gov/visible/bitmaps/color24/

I will get some more files next week, and they are probably in dicom format,

but maybe I can get them in raw format as well (if this makes things more easy).

Simon,

I've found some tools allowing to view the files, and there are many which allow

a conversion to a 3d model, but I wanted to try to do as much as possible in houdini

(if possible at all).

The marching cubes software you talked about, is this the part where the raw files get

convertet to geometry?

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The marching cubes software you talked about, is this the part where the raw files get

convertet to geometry?

15309[/snapback]

Yup. Very similiar to what the iso sop does, only it deals with much bigger data sets easier. It's custom code though I'm afraid.

I think dicom can be read into photoshop as raw..... don't quote me though. For some reason Houdini can't read raw as far as I know.

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