A simple utility to visualize 3D NIFTI image based on Python3.
All you need is the "nll_preview.py" located in this repo.
Copy "nll_preview.py" into your project directory and everything is done :). But also, you need to install the following Python packages (ignore if you already installed):
- matplotlib (any version should work)
- numpy (any version should work)
- nibabel (used for loading "*.nii" or "*.nii.gz" files, recommend version >=3.2.1, but lower version is OK I guess)
here is an example of how to use it
Below is an example of using "lightbox()" function to generate a preview of a 3D NIFTI file. "view_axis" is set to "coronal". Note that slice number is also indicated in the upper left corner. I carefully adjusted the behaviour of "lightbox()" to ensure that the visualization result is the same with that of MIPAV and ITK-SNAP.
Now I added support for image resampling (for propoerly visualizing images with anisotropic resolution) and color overlays (such as visualizing lesions).
Example:
# Draw red mask (255,0,0) on image, also resample the image to have isotropic resolution
# (0.5mm*0.5mm*0.5mm in this example), setting font size (x2 than normal size) and blend weight (=0.5),
# coronal view. 4 rows, 5 columns.
lightbox('original_image.nii.gz', 4,5,'test_lightbox3.png',view_axis='coronal',
nii_mask='segmentation.nii.gz', color_palette=[(255,0,0)],blend_weight=0.5,
resample=0.5, font_size=2)
Will generates the following output:
