New user: Loading non-dicom data

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?

  • Cam

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

3.92 GB of PNG’s

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

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

There are 2,973 png’s

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

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

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

@pieper @hherhold

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