NIfTI-1 (.nii) import

[mlavik1]

Add support for importing NIfTI-1 datasets.

Data format specification: https://nifti.nimh.nih.gov/nifti-1 Test data sets: https://nifti.nimh.nih.gov/nifti-1/data Example of a NIfTI-1 file reader: https://github.com/Enet4/nifti-stream

[iowagrade]

I will take a look at this issue. In issue #36, you referenced exporting the files as a .jpg dataset. Can you provide more information on what software you used for import/export of the files? I tried installing darktable to utilize with gimp to read .raw files, but didn't have straightforward luck. Can you mention which software you use with .raw files? I will also take a look at issue #53 with importing NRRD files and see if I can locate the synergy amongst the tasks.

[mlavik1]

Hi, Thank you, that would be great! I really appreciate any contributions I can get. I'm not at all familiar with the NIfTI-1 format (I added this task after receiving a feature request for it), but let me know if there's anything else I can assist with :)

And I think that issue is not related to this. In #36 I just opened the link to the DICOM dataset Chiara shared (https://www.dicomlibrary.com/meddream/?study=1.2.826.0.1.3680043.8.1055.1.20111102150758591.92402465.76095170) and exported the dataset as a JPEG image sequence. So I didn't use any software to open .raw files. But if I remember correctly, ImageVis3D has that feature! This project also has a RAW importer by the way: https://github.com/mlavik1/UnityVolumeRendering/blob/master/Assets/Scripts/Importing/RawDatasetImporter.cs

By the way, for all import-related tasks please keep in mind that it needs to work cross platform (Windows, Linux, MacOS, and ideally Android too) out of the box. Using a large library like SimpleITK could then be a potential issue, since it will take up a lot of space and we need to build and host the .dll/.so files somewhere. So it's best to avoid dependencies to large libraries, especially native (not .NET) ones, as much as possible. If it's needed, please let me know so we can try to come up with a good solution.

[Contused]

Hi, I worked with your plugin last year and built a little nifti importer on top. I used the https://github.com/plwp/Nifti.NET as a .dll library. If you think this can be any help to you, we can get in contact.

[mlavik1]

Hi! Thanks for mentioning this! I didn't know about this library. I'm actually working on adding an optional integration of the SimpleITK library, which supports NIFTI import. However, the problem with SimpleITK is that it's a native library, and won't automatically work on all platforms, unless I build binaries for that platform. So It would be good to have a non-native library to use on these platforms as well, and NIFTI.net seems like a great alternative! Do you have an open fork that I can look at?

[Contused]

I just forked the project and added my editor script. I also added 2-3 sentences to the readme about the intended import process. Please consider that the script was made for a private prototype to import a certain dataset. It´s nowhere near polished. Much work has to be done to properly integrate the importer into your project and get it to work for all nifti datasets. https://github.com/Contused/UnityVolumeRendering

[mlavik1]

Thank you, this is very useful! I will take a look at this when I have finished my SimpleITK-related work. I've changed the importer interface in that branch a bit.

[mlavik1]

Closing, since we now have both the SimpleITK importer (that supports Nifti), as well as a non-native importer for other platforms.