Exporting MATLAB data for gel dosimetry

Hi there,

I am running an in-house MATLAB program to reconstruct optical CT files. The only options this program has to save the reconstructions are “save as type: All MATLAB files” or “export cube” which generates a .raw file. I am trying to use the Gel Dosimetry slicelet and the tutorial calls for a .VFF file (and the slicelet itself says “Load optical CT files from VFF, NRRD, etc.”. I have everything else for the slicelet to run (Normal CT image, struct, planned dose from Eclipse, etc.) but I am struggling with how to possibly import my actual reconstructed, irradiated scan.

Does anyone out there have experience with this?

Thank you!

You can save the image matrix in Matlab as a nrrd file, for example using nrrdwrite.m.

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Thank you for the response!

I’m not sure how to utilize this function however. The .mat file that is saved is a 1x1 struct . I tried to set the “img” argument equal to this struct (in the workspace) but I got an error of “Reference to non-existent field ‘pixelData’.” My Matlab knowledge is extremely slim and this is all new territory for me, am I even using this function correctly?

Usage instructions are described in great details in the function’s documentation:

Matlab is on a steep decline. Instead of investing time into learning it, you might consider using existing sophisticated image reconstruction solutions implemented in C++ and available in Python, for example RTK (Python package: itk-rtk).


I’ve tried to make this work with what I can export using this custom GUI built in Matlab (basically a 3D matrix, .mat file) but I’ve had no success. Instead, I’ve written the .mat out to a dicom and am attempting to use this as the measured/calibration data in the gel dosimetry slicelet. It seems to be working so far, is there any reason a non dicom should be used?

Thank you!