New user: Loading non-dicom data

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Hi Slicer community. I am an undergraduate student assisting in research and I am brand new to 3D modeling. Our research involves scans of fish and we have 10 or so folders with the scan data. The only downside that I have seen is that none of the files are in .dcm format. Instead, they are in .tif or .png files. When I try to load this non-dicom data, the application ends up crashing and I have only been able to load around 500 png’s at a time. Does anyone have any advice on possibly how to convert png to another file type or useful extensions?
Thanks!

  • Cam
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TIFF and PNG files should work fine. How much memory, what kind of CPU, etc?

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3.92 GB of PNG’s

Processor Intel(R) Xeon(R) Gold 6240R CPU @ 2.40GHz 2.39 GHz
32 GB ram

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OK, that should work. How many PNG files, and what are their dimensions? (i.e., what are the dimensions of your stack)?

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There are 2,973 png’s

If by dimensions you mean pixels it is 2436 x 2088.

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You can try the ImageStacks module in SlicerMorph: SlicerMorph/Docs/ImageStacks at master · SlicerMorph/SlicerMorph · GitHub. It was designed for this purpose and allows you to subset or resample the data while loading to save memory.

1 Like
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I’d highly recommend Steve @pieper’s suggestion. ImageStacks works great.

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@pieper @hherhold

I will give SlicerMorph a try and let you know how it goes. I appreciate your fast and knowledgeable replies!