plwp / nifti.net

A basic library for reading, writing and manipulating NIfTI files.

Nifti.NET

A basic library for reading, writing and manipulating NIfTI files.

(If you're looking for the TensorFlow CNN platform, try NiftyNet (https://niftynet.io/))

nifti.net's Issues

Writing Unity3D Texture3D to NIfTI file

Thanks for making this code available. I have a Unity3D app that use the VolumeViewPro Unity Asset to load multiple NIfTI files and display them in VR. These images are viewed an manipulated leading to changes in the underlying image data. So now I want to write a new Texture3D back out as a new NIfTI file. Not having any success yet...

I'm a middle level programmer so I may have missed some obvious way to use your NiftiFile.Write() routine. Texture3Ds are 3D array of Colors. After trying a number of variants, I can't figure out how to convert the Color array, nor what the proper datatype to use in your write file.

The error I get is:

System.Object.CallSite.Target(System.Runtime.CompilerServices.Closure,System.Runtime.CompilerServices.CallSite,System.Type,System.IO.Stream,object)
System.Dynamic.UpdateDelegates.UpdateAndExecuteVoid3[T0,T1,T2] (System.Runtime.CompilerServices.CallSite site, T0 arg0, T1 arg1, T2 arg2) (at <3e4da02cf86b4fc686ed0ac61bffc210>:0)
Nifti.NET.NiftiFile.Write (Nifti.NET.Nifti nifti, System.String path, System.Boolean gzip) (at Assets/NiftiFile.cs:78)

Any help greatly appreciated.

!!!----- Urgent -----!!! please help me

create a 3d Nifti viewer using the Library

i want to create an 3d Nifti Image Format Viewer ,it is possible to do that using the Nifti.net library if yes how can i convert the NiftiFile.Read(path); result to a 3d Bitmap

Thanks in advance

NiftiFile.Write throw Exception when gzip=true

GZipStream.Position NotSupportedException

Incorrect Import of unsigned short (uint16) datasets

When importing a uint16 dataset the library creates a data array twice the correct size. Furthermore the values inside the array are shifted. Both the dimensions and datatype are being read correctly from the header. The "forcetype" parameter does not seem to work.

I tested the same dataset inside a different application and it worked fine.

To recreate the problem you can use the "wallnut.nii.gz" dataset provided by the University of Leipzig, Germany:

http://www.informatik.uni-leipzig.de/~wiebel/public_data/index.html

They also have the open source software called "OpenWalnut" to display the dataset:

http://www.openwalnut.org/

Technical details:
-Nifti.Net is used as a dll for a C# Script in Unity 2019.4.12f11
-Nifti.Data.Length return twice the correct size of the imported dataset array
-Dimensions and datatype are correct
-forcetype parameter in Nifti.Read does not change the outcome
-You can iterate past the size of a dimension in the dataset
-Displaying the dataset shows that the values are shifted in a certain pattern
-uint8 datasets are working fine with the lib

Time frame , the length of each frame is different, how to deal with the NII format.

Time frame, the length of each frame is different, how to deal with the NII format.
For example, the time of the first frame is 0-5s, and the time of the second frame is 5-25s。

about API document

When you encounter some problems in use, can you write an API document?

Would be handy to be able to create a new Nifti object from data

Maybe see how nibabel populates the q_form and s_form values from a given affine matrix.

Saves us having to rely on file templates (which can be annoying).