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simulation and reconstruction package
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phantom.mhd #100

Open omrghad opened 2 weeks ago

omrghad commented 2 weeks ago

dear all, please i have a chest phantom in form .mhd, how can i import it on XCIST for use it in simulation regards

MingyeWu commented 2 weeks ago

Hi omrghad, could you explain what is the .mhd phantom?

omrghad commented 1 week ago

dear MingyeWu, it is MetaImage format : header. mhd + raw image .raw (voxelized phantoms), a chest phantom attached below ( i converted CT slice (HU) to Electronic density) and stuck it to form a phantom. phantom.zip else, if there s a patient phantoms compatible with XCIST, please provide me the link regards

zhangjy-ge commented 1 week ago

you may define your own voxelized phantom, given that you already have this in .mhd file. Please check an example voxelized phantom here: https://github.com/xcist/example/tree/main/AAPM_datachallenge/simulation_scripts

in which *json file defines material names, voxel size, density etc, and the phantom.vf file has volume fraction information of the voxelized phantom. You may also check another example here: https://github.com/xcist/main/tree/master/gecatsim/phantom/CatSimLogo_1024

PaulFitzGerald commented 1 week ago

Please pay careful attention to the last part of Jiayong's reply - this sometimes causes confusion. The units of the phantom files (one file for each material in the phantom) need to be the VOLUME FRACTION of the material specified in each file associated with the phantom.

Paul

On Tue, Sep 24, 2024, 6:54 PM Jiayong Zhang @.***> wrote:

you may define your own voxelized phantom, given that you already have this in .mhd file. Please check an example voxelized phantom here: https://github.com/xcist/example/tree/main/AAPM_datachallenge/simulation_scripts

in which *json file defines material names, voxel size, density, and the phantom.vf file has volume fraction information of the voxelized phantom.

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omrghad commented 1 week ago

dear all, thank you for your reply, really i did not arrive to convert .mhd phantom to .json and .vf files, i tried also with dicom image to phantom (.json and .vf) but i did not get the results. any help of how to convert this phantom to XCIST phantom? thank you again regards

zhangjy-ge commented 4 days ago

I am not sure how your json file looks like, but it should be like this: https://github.com/xcist/main/blob/master/gecatsim/phantom/CatSimLogo_1024/CatSimLogo_1024_128mmZ.json

A very important parameter in this file is volumefractionmap_filename, which should direct to a binary file, let's say water_512x512x1.vf (the file extension does not matter), in which it specifies the volume fraction of water in a 512x512x1 voxel volume. Each voxel size is defined by x_size, y_size, z_size. Volume fraction of 1 means this voxel has 100% water, of 0.5 means it only has 50% water (other 50% could be air or bone). You can specify multiple materials, as shown in the file.

When you have a problem, please don't forget to clearly state what you have done/tried, what output you got or what error messages you got, and post your files, so that we can better understand your situation and help you.