Using volume import module for 3D Slicer to extract image stacks from .vol files

Hello everyone,

I’m pretty new to using the 3D slicer software and recently downloaded it to convert .vol files to image stacks using this plugin by @muratmaga:

I managed to already visualize my data in the program after generating an NHDR file. However, I still don’t quite know how to extract image stacks using this plugin. I tried to then save the scene in the .TIFF format, but when I do so, I only get one single image file that I can’t open containing all the data.

Unfortunately, I don’t have any programming experience with Python and many previous posts I saw related to my issue discussed some Python scripts to solve this. So if anyone knows a different and more simple solution to this issue, I’d appreciate your input!

NRRD (or NHDR) file format can store an image stack in a convenient single-file format, preserving essential 3D geometry information. Therefore, in general you don’t want to downgrade to storing the image in a stack of TIFF files.

Can you describe your overall goal? What software are you planning to use for analyzing a TIFF stack?

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I’m planning to segment the data using the Dragonfly software and previously, with other data sets, I’ve always used TIFF image stacks for that. I have not seen the option to load NHDR files into Dragonfly.

You can load NIFTI images (saved in Slicer as .hdr file) into Dragonfly. I would suggest to submit a feature request for Dragonfly for NRRD loading, as it is very easy to implement and a basic requirement for an image computing research software.

In general Slicer is much more capable software than Dragonfly: it has much more features and it is free and customizable and extensible. Is there any specific feature of Drafonfly that you don’t find in Slicer?

Thank you, I’ll try that out.

Regarding the softwares, I’ve just always worked with Dragonfly in the past and the video editing in Dragonfly is very smooth. In Slicer, I have yet to get acquainted with all the different features and the segmentation options.