How to perform image processing on raw DICOM medical data?

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I have received a raw DICOM medical pet data with over 5000 files. I would like to perform image processing on them in MATLAB. I have tried to adjust the threshold level in AMIDE but I have no idea whether to convert them to .dcm or .xif. Each file has 25 time frames.
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Image Analyst
Image Analyst 2016-1-3
What is AMIDE? How are thresholds determined in it?
When you say "them", to what do you refer? To the threshold levels (which is the subject of that sentence)?

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Walter Roberson
Walter Roberson 2016-1-3
Use dcm files. In MATLAB, use dicomread(). The output of that will be a 4D array, width by height by 1 by timestep

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