Create nice looking gifs from your nifti (.nii or .nii.gz) files with a simple command:
gif_your_nifti /path/to/data.nii
| Package | Tested version |
|---|---|
| NumPy | 1.14.2 |
| NiBabel | 2.2.1 |
| matplotlib | 2.2.0 |
| imageio | 2.2.0 |
| scikit-image | 0.13.0 |
The quickest method is to install directly from GitHub:
pip install git+https://github.com/miykael/gif_your_nifti.gitAlternately, navigate to the main page of the repository and clone it. Then, change directory to the cloned repository and run:
pip install . # If you're not making changes
# or
pip install -r requirements.txt # If you're a developerBuild a docker container with:
docker build -t gif_your_nifti .Run with docker:
docker run --rm -v /path/to/nifti/:/data gif_your_nifti:latest /data/image.niiFor the examples below, I've downloaded ICBM 2009c Nonlinear Asymmetric and used the T1 and gray matter template thereof.
It is also possible to use your own brain image, as I will show below. The only thing that you need to make sure is, that your brain image has the right orientation. You can reorient your NIfTI image according to the MNI template standard with the FSL command: fslreorient2std my_brain.nii my_brain.nii.
To create a simple gray scale gif, type the following command in your commandline:
gif_your_nifti /path/to/mni_icbm152_t1_tal_nlin_asym_09c.nii
To create a pseudocolor gif, type the following command in your commandline:
gif_your_nifti /path/to/Me_2014.nii --mode pseudocolor --cmap plasma
The colormap can be any colormap from the matplotlib colormaps.
To create a depth gif, type the following command in your commandline:
gif_your_nifti /path/to/mni_icbm152_t1_tal_nlin_asym_09c.nii --mode depth
The image shows you in color what the value of the next slice will be. If the color is slightly red or blue it means that the value on the next slide is brighter or darker, respectifely. It therefore encodes a certain kind of depth into the gif.
To create a Red Blue Green (RGB) gif, type the following command in your commandline:
gif_your_nifti /path/to/gm.nii /path/to/wm.nii /path/to/csf.nii --mode rgb
This image takes the values from the first NIfTI file as its red colors, second NIfTI file as its green colors and third NIfTI as its blue colors.
It is also possible to change the size of a gif, by changing the size parameter in any function above. The following are examples of resizing the images to 50% of it's original size, with:
gif_your_nifti /path/to/mni_icbm152_gm_tal_nlin_asym_09c.nii --size 0.5
gif_your_nifti /path/to/mni_icbm152_gm_tal_nlin_asym_09c.nii --size 0.5 --mode pseudocolor --cmap cubehelix
gif_your_nifti /path/to/mni_icbm152_gm_tal_nlin_asym_09c.nii --size 0.5 --mode pseudocolor --cmap inferno
gif_your_nifti /path/to/mni_icbm152_gm_tal_nlin_asym_09c.nii --size 0.5 --mode pseudocolor --cmap viridis
Changing the size of a gif also changes the frames per second parameter, so that the overall tempo stays the same. Meaning, if you have a gif of original size with 20 frames per second (fps), changing the size to 50%, will cause the smaller gif to run at 10 fps, so that both take the same amount for a cycle.
You can also use gif_your_nifti from a python script. See script examples for further information.
This project is licensed under BSD 3-Clause License.